Author: "Jérôme Salse" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

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1. Population genomics of apricots unravels domestication history and adaptive events

Author: Patrick Wincker, Corinne Cruaud, William Marande, Guillaume Roch, Amandine Cornille, Nathalie Rodde, Jean-Marc Aury, Robert Debuchy, Quynh Trang Bui, David Tricon, Pierre Pétriacq, Jérôme Salse, Rémy Félix Serre, Sandrine Arribat, Tatiana Giraud, Alexis Groppi, Erwan Denis, Wassim Rhalloussi, Céline Lopez-Roques, Véronique Decroocq, Olivier Bouchez, Shuo Liu, Macha Nikolski, Jean Marc Audergon, Sébastien Carrère, Xilong Chen, Patrick Lambert, Caroline Belser, Cecile Huneau, Stéphane Decroocq, Tetyana Zhebentyayeva, Stéphane Cauet, Weisheng Liu, Joseph Tran, Benjamin Istace, Albert G. Abbott, Aurélien Barré, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Institute of Pomology (RIP CAAS), Chinese Academy of Agricultural Sciences (CAAS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), CEP Innovation, The Schatz Center for Tree Molecular Genetics,Department of Ecosystem Science and Management, The Pennsylvania State University, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forest Health Research and Education Center,University of Kentucky, (FHC), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-CHEX-0002,ABRIWG,Génomique comparative et fonctionnelle de la résistance à la sharka et des besoins en froid chez les arbres fruitiers à noyaux(2011), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Pennsylvania State University (Penn State), Penn State System, Liaoning Institute of Pomology, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), University of Kentucky (UK), GET-PACBIO program (« Programme opérationnel FEDER-FSEMIDI-PYRENEES ET GARONNE 2014-2020 »), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Gauthier, Muriel, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Université Bordeaux Segalen - Bordeaux 2-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sciences et Technologies - Bordeaux 1, Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Kentucky
Subjects: 0106 biological sciences, 0301 basic medicine, Prunus armeniaca, [SDV]Life Sciences [q-bio], General Physics and Astronomy, adaptation, 01 natural sciences, Gene flow, Population genomics, Plant evolution, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Arbre fruitier à noyau, Génétique, Phylogeny, Disease Resistance, Multidisciplinary, biology, Phylogenomics, [SDV] Life Sciences [q-bio], Génomique, Phenotype, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene pool, Fruit à noyau, Genome, Plant, Gene Flow, Agricultural genetics, Abricotier, Science, Chromosomes, Plant, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, domestication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Domestication, Abricot, Life Cycle Stages, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genetic Variation, General Chemistry, Phenotypic trait, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Evolutionary biology, Fruit, Metagenomics, Adaptation, divergence, 010606 plant biology & botany
Abstract: Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding., The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.
Published: 2021

2. Episodes of gene flow and selection during the evolutionary history of domesticated barley

Author: Terence A. Brown, Konstantina Drosou, Jérôme Salse, Wandrille Duchemin, Peter Civáň, David Armisen-Gimenez, Department of Earth and Environmental Sciences, The University of Manchester, University of Manchester [Manchester], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Faculty of Biology, Medicine and Health [Manchester, UK], Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Computer Science (University of Basel), University of Basel (Unibas), European Research Council grant 339941, and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, lcsh:QH426-470, lcsh:Biotechnology, Population, Subspecies, Biology, 01 natural sciences, Gene flow, Domestication, Crop, Fertile Crescent, 03 medical and health sciences, lcsh:TP248.13-248.65, Barley, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Exome sequences, education, Selection, Selective sweep, Phylogeny, Selection (genetic algorithm), 030304 developmental biology, Hordeum vulgare, 2. Zero hunger, 0303 health sciences, education.field_of_study, Origins of agriculture, food and beverages, Hordeum, 15. Life on land, Biological Evolution, lcsh:Genetics, Evolutionary biology, [SDE]Environmental Sciences, Research Article, 010606 plant biology & botany, Biotechnology
Abstract: BackgroundBarley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop.ResultsWe examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups.ConclusionsIdentification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as ‘domestication traits’. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.
Published: 2021

3. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author: Pierre-Marc Delaux, Romain Guyot, Martin Crespi, Erika Sallet, Malika Laguerre, Fanchon Divol, Sébastien Carrère, Benjamin Péret, Patrick Doumas, Cecile Huneau, Matthew R. Nelson, Jemma Taylor, Alexandre Soriano, Jérôme Salse, Laurence Marquès, Veit Schubert, Fernando Geu-Flores, Davide Mancinotti, Jérôme Gouzy, Sandrine Arribat, Karine Gallardo, André Marques, Thomas Blein, Barbara Hufnagel, William Marande, Delphine Aime, Hélène Bergès, Jean Keller, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), The University of Western Australia (UWA), Centre IRD de Montpellier (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), VILLUM Foundation : 15476, Innovate UK, FAPEAL/CNPq (Brasil), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), European Project: 0637420(2007), University of Copenhagen = Københavns Universitet (UCPH), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens [Kew], and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0106 biological sciences, 0301 basic medicine, Repetitive Sequences, Nucleic Acid/genetics, Plant Roots/genetics, [SDV]Life Sciences [q-bio], Plant genetics, Gene Dosage, General Physics and Astronomy, Sequence assembly, Alkaloids/chemistry, Plant Roots, 01 natural sciences, Genome, Lupinus, Soil, Nutrient, Gene Duplication, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Plant Proteins/metabolism, 2. Zero hunger, Multidisciplinary, Ecotype, food and beverages, Transcriptome/genetics, Polymorphism, Single Nucleotide/genetics, Seeds, Genome, Plant, Agricultural genetics, Synteny/genetics, Plant domestication, Science, Centromere, Biology, Lupinus/genetics, Polymorphism, Single Nucleotide, Synteny, Article, General Biochemistry, Genetics and Molecular Biology, Crop, Evolution, Molecular, 03 medical and health sciences, Alkaloids, Seeds/physiology, Centromere/genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Repetitive Sequences, Nucleic Acid, Models, Genetic, fungi, Genetic Variation, Molecular Sequence Annotation, General Chemistry, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Plant Leaves, 030104 developmental biology, Agronomy, Genomic Structural Variation, lcsh:Q, Plant Leaves/metabolism, Transcriptome, 010606 plant biology & botany
Abstract: White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield., White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
Published: 2020

4. Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour

Author: Kirsty L. Hassall, Marianna Rakszegi, Till K. Pellny, Michelle Leverington Waite, Alison Lovegrove, Amy Plummer, Abigail J. Wood, Luzie U. Wingen, Ondrej Kosik, Gilles Charmet, Rowan A. C. Mitchell, Peter R. Shewry, Karolina Tremmel-Bede, M.R. Perretant, Caroline Pont, Amanda J. Burridge, Zoltán Bedő, Simon Orford, Jackie Freeman, Simon Griffiths, Mehmet Ülker, Diana Passmore, Jérôme Salse, Rothamsted Research, John Innes Centre [Norwich], Yüzüncü Yıl University, Van, Turkey, Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bristol [Bristol], and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0106 biological sciences, Germplasm, [SDV]Life Sciences [q-bio], Flour, Physical Chemistry, 01 natural sciences, chemistry.chemical_compound, Materials Physics, Arabinoxylan, Medicine and Health Sciences, Food science, Cultivar, Triticum, 2. Zero hunger, 0303 health sciences, education.field_of_study, Multidisciplinary, Viscosity, Physics, Eukaryota, Chromosome Mapping, food and beverages, Genomics, Bread, Plants, Chemistry, Wheat, Physical Sciences, Medicine, Xylans, Research Article, Genetic Markers, Science, Materials Science, Quantitative Trait Loci, Population, Wheat flour, Quantitative trait locus, Biology, Research and Analysis Methods, Chromosomes, Plant, Transgressive segregation, 03 medical and health sciences, Genetics, Genome-Wide Association Studies, Grasses, Molecular Biology Techniques, education, Molecular Biology, Alleles, Crosses, Genetic, Nutrition, 030304 developmental biology, Gene Mapping, fungi, Organisms, Biology and Life Sciences, Computational Biology, Reproducibility of Results, Human Genetics, Genome Analysis, Diet, Chemical Properties, chemistry, Food, Genetic Loci, Genetic marker, Lod Score, Genome-Wide Association Study, 010606 plant biology & botany
Abstract: International audience; Dietary fibre (DF) has multiple health benefits and wheat grains are major sources of DF for human health. However, DF is depleted in white wheat flour which is more widely consumed than wholegrain. The major DF component in white flour is the cell wall polysaccharide arabinoxylan (AX). We have identified the Chinese wheat cultivar Yumai 34 as having unusually high contents of AX in both water-soluble and insoluble forms. We have therefore used populations generated from crosses between Yumai 34 and four other wheat cultivars, three with average contents of AX (Ukrainka, Altigo and Claire) and one also having unusually high AX (Valoris), in order to map QTLs for soluble AX (determined as relative viscosity of aqueous extracts of wholemeal flours) and total AX (determined by enzyme fingerprinting of white flour). A number of QTL were mapped, but most were only detected in one or two crosses. However, all four crosses showed strong QTLs for high RV/total AX on chromosome 1B, with Yumai 34 being the increasing parent, and a KASP marker for the Yumai 34 high AX allele was validated by analysis of high AX lines derived from Yumai 34 but selected by biochemical analysis. A QTL for RV was also mapped on chromosome 6B in Yumai 34 x Valoris, with Valoris being the increasing allele, which is consistent with the observation of transgressive segregation for this population. Association studies in an independent germplasm panel identified marker trait associations for relative viscosity in these same locations while direct selection for fibre content in breeding resulted in high levels of enrichment for the Yumai 34 1B allele. The data therefore indicate that marker-assisted breeding can be used to develop wheat with high AX fibre in white flour.
Published: 2020

5. The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

Author: Shan Wu, Z. J. Wu, Honghe Sun, Xuelian Sui, Amnon Levi, Shamimuzzaman, Zhangjun Fei, Alan Wilder, Jérôme Salse, Kai-Shu Ling, Yong Xu, Wuhan Technology and Business University, Natl Engn Res Ctr Vegetables, Key Lab Biol & Genet Improvement Hort Crops N Chi, Beijing Acad Agr & Forestry Sci, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Vegetable Lab, United States Department of Agriculture, Bio-Computing Research Center, Harbin Institute of Technology (HIT), Boyce Thompson Inst Plant Res, Cornell University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Boyce Thompson Institute [Ithaca], and Cornell University [New York]
Subjects: 0301 basic medicine, Genome evolution, [SDV]Life Sciences [q-bio], Potyvirus, Locus (genetics), Plant Science, Genome, Chromosomes, Plant, Papaya ringspot virus, 03 medical and health sciences, Cucurbita, Cleaved amplified polymorphic sequence, Botany, Genetics, cucurbit genome evolution, ComputingMilieux_MISCELLANEOUS, Disease Resistance, Plant Diseases, 2. Zero hunger, Comparative genomics, Papaya ring-spot virus resistance, biology, Chromosome Mapping, Lagenaria, Cell Biology, 15. Life on land, biology.organism_classification, Biological Evolution, genome sequencing, Cucurbitaceae, 030104 developmental biology, Lagenaria siceraria, Genetic Loci, bottle gourd, Genome, Plant
Abstract: Summary Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstruct the genome of the most recent common ancestor of Cucurbitaceae, which reveals that the ancestral Cucurbitaceae karyotypes consists of 12 protochromosomes with 18,534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The eleven bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ringspot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement. This article is protected by copyright. All rights reserved.
Published: 2017

6. Tracing the ancestry of modern bread wheats

Author: David Armisen, Jérôme Salse, Luigi Cattivelli, Daniela Bustos-Korts, Alessandro Tondelli, Darren Waite, Daniel Lang, Fred A. van Eeuwijk, Gilles Charmet, Thomas Letellier, Manuel Spannagl, Sarah Dyer, Jacob Lage, Nils Stein, Michael Alaux, Robbie Waugh, Thibault Leroy, Joanne Russell, Hakan Özkan, Caroline Pont, François Balfourier, Beat Keller, Benjamin Kilian, Klaus F. X. Mayer, Nadia Goué, Michael Seidel, Wandrille Duchemin, Georg Haberer, Márta Molnár-Láng, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [Bolivie]), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), PGSB, Helmholtz Zentrum München = German Research Center for Environmental Health, Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Biometris, Applied Statistics, Wageningen University and Research [Wageningen] (WUR), Agricultural Institute [Budapest] (ATK MGI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), KWS UK Ltd, Global Crop Diversity Trust, Earlham Institute, National Institute of Agricultural Botany (NIAB), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), The James Hutton Institute, Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Leibniz Institute of Plant Genetics and Crop Plant Research, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Helmholtz Center Munich, Council for Agricultural Research and Economics (CREA), Wageningen University and Research Center (WUR), University of Çukurova, University of California [Berkeley], University of California-University of California, Çukurova Üniversitesi, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Helmholtz-Zentrum München (HZM), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: [SDV]Life Sciences [q-bio], Population genetics, Biology, Wiskundige en Statistische Methoden - Biometris, Domestication, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, blé, Exome Sequencing, Genetic variation, Genetics, Life Science, Cultivar, Plant breeding, évolution, paleo-génomique, Mathematical and Statistical Methods - Biometris, Phylogeny, Triticum, Selection (genetic algorithm), Exome sequencing, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Models, Genetic, génome, digestive, oral, and skin physiology, Genetic Variation, food and beverages, Bread, 15. Life on land, PE&RC, Plant Breeding, Biometris, Evolutionary biology, Adaptation, Genome, Plant, 030217 neurology & neurosurgery
Abstract: PubMedID: 31043760 For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world’s most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement. © 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. 339728 Kyoto University California Department of Fish and Game: SFB924 Wageningen UR University of Dundee 2819103915 Région Auvergne-Rhône-Alpes European Research Council 23000816 SRESRI 2015 Seventh Framework Programme: FP7-613556, FP7/ 2007–2013 23000892 SYMBIOSE 2016 Agence Nationale de la Recherche: 14-CE02-0002 Çukurova Üniversitesi: FUA-2016–6033 The authors wish to thank the INRA Biological Resources Center on small grain cereals (https://www6.ara.inra.fr/umr1095_eng/Teams/Research/Biological-Resources-Centre) for providing seeds and passport data, and for establishing a wheat biorepository. The authors thank the Federal ex situ Genbank Gatersleben, Germany (IPK), the N. I. Vavilov All-Russian Research Institute of Plant Industry, Russia (VIR), Centre for Genetic Resources, WUR, Netherlands (CGN), Kyoto University, National Bioresource Project, Japan (NBRP), the Australian Winter Cereal Collection Tamworth, Australia (AWCC), the National Plant Germplasm System, USA (USDA-ARS), the International Center for Agriculture Research in the Dry Areas (ICARDA), the Max Planck Institute for Plant Breeding Research Cologne, Germany (MPIPZ), Germplasm Resource Unit at the John Innes Centre UK (JIC) and the Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium for providing plant material and passport data. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/ 2007–2013) under grant agreement FP7-613556, Whealbi project (http://www.whealbi.eu/project/). R.W. and J.R. also acknowledge support from the Scottish Government Research Program and R.W. from the University of Dundee. H.O. acknowledges support from Çukurova University (FUA-2016–6033). K.F.X.M. acknowledges support from the German Federal Ministry of Food and Agriculture (2819103915) and the DFG (SFB924). T.L. acknowledges supports from the Agence Nationale pour la Recherche (BirdIslandGenomic project 14-CE02-0002), European Research Council (TREEPEACE project, grant agreement 339728) and the bioinformatics platform from Toulouse Midi-Pyrénées (Bioinfo Genotoul) for providing computing and storage resources. J.S. acknowledges support from the Région Auvergne-Rhône-Alpes and FEDER Fonds Européens de Développement Régional (23000816 SRESRI 2015), the CPER contrat de plan État-région (23000892 SYMBIOSE 2016) and AgreenSkills fellowship (applicant ID 4146).
Published: 2019

7. Genome sequence of the cluster root forming white lupin;

Author: Barbara Hufnagel, Benjamin Péret, Pierre-Marc Delaux, Patrick Doumas, Romain Guyot, Alexandre Soriano, William Marande, Sandrine Arribat, Hélène Bergès, Laurence Marquès, Malika Laguerre, Thomas Blein, Erika Sallet, Davide Mancinotti, Martin Crespi, Sébastien Carrère, Matthew R. Nelson, Cecile Huneau, Jérôme Salse, Jemma Taylor, Fanchon Divol, Jean Keller, Fernando Geu-Flores, Delphine Aime, Veit Schubert, Karine Gallardo, Jérôme Gouzy, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Royal Botanic Gardens [Kew], Leibniz Institute of Plant Genetics and Crop Plant Research, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Copenhagen = Københavns Universitet (KU), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Royal Botanic Gardens, Kew, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Développement et Plasticité du Système Racinaire (PLASTICITE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen, Frederiksberg C, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (UNS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, Root system, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Lupinus, Symbiosis, Arabidopsis, Botany, Cluster root, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Legume, 030304 developmental biology
Abstract: White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well asde novoassemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify theAPETALA2transcription factorLaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.
Published: 2019

8. Development of new SSR markers for homoeologous WFZP gene loci based on the study of the structure and location of microsatellites in gene-rich regions of chromosomes 2AS, 2BS, and 2DS in bread wheat

Author: Yu. L. Orlov, Caroline Pont, Jérôme Salse, and O. B. Dobrovolskaya
Subjects: 0106 biological sciences, 0301 basic medicine, Genetics, food and beverages, Biology, 01 natural sciences, Genome, DNA sequencing, Human genetics, 03 medical and health sciences, 030104 developmental biology, Genetic marker, Microsatellite, Animal Science and Zoology, Mobile genetic elements, Agronomy and Crop Science, Gene, Function (biology), 010606 plant biology & botany
Abstract: Microsatellites, or simple sequence repeats, are widely distributed in eukaryotic genomes, including plant genomes. The peculiarities of the structure and location of the microsatellite loci determine their potential as molecular genetic markers and can influence the assumed function of microsatellites in important biological processes. The identification and study of the distribution of microsatellite loci in gene-rich genome regions of the bread wheat and the development (based on them) of new microsatellite markers are of practical interest and are important for the study of the organization of the bread wheat genome. The sequences of BAC clones that contain the homoeologous WFZP genes of the bread wheat (Triticum aestivum L.) controlling the development of the ear were the basis for the identification and localization of microsatellite loci in gene-rich regions of the 2AS, 2BS, and 2DS chromosomes. Diand trinucleotide microsatellite repeats are the most widespread in the studied sequences. The AG and GA/TC motifs prevail among the dinucleotide motifs; the dinucleotide repeats are found in noncoding gene regions, mobile elements, and nonannotated DNA sequences. Most of the trinucleotide repeats are associated with mobile genetic elements. It was found that homoeologous microsatellite loci are located either in the genes or in the nonannotated DNA sequences. The comparison of the structure of homoeologous loci demonstrated that the divergence in them is associated both with a change in the number of repeats and with nucleotide substitutions. The new microsatellite markers, which are colocalized in the genetic maps with the WFZP-A-B-D genes and can be used for marking these genes in molecular genetic studies and in breeding controlled by markers, were developed.
Published: 2016

9. The Rosa genome provides new insights into the domestication of modern roses

Author: Sylvie Baudino, Caroline Pont, Arnaud Lemainque, Michiel Vandenbussche, Jean-Claude Caissard, Teva Vernoux, Patrick Wincker, Florence Piola, Chang Liu, Hélène Badouin, Adnane Boualem, Mohammed-Amin Madoui, Moussa Benhamed, Jean-Marc Aury, Jérôme Salse, Abdelhafid Bendahmane, Manuel Le Bris, Benjamin Govetto, Hadi Quesneville, Olivier Raymond, Jérôme Gouzy, Mohammed Bendahmane, Sandrine Moja, Annick Dubois, Judit Szécsi, Priscilla Villand, Claudia Bardoux, Shu-Hua Yang, Céline Lopez-Roques, Ludovic Cottret, Pascal Heitzler, Antoine Larrieu, Véronique Boltz, Nathalie Choisne, Yoan Labrousse, Léa François, David Latrasse, Marion Verdenaud, Lauriane Perrier, Philippe Vergne, Sébastien Carrère, Magali Perez, Karine Labadie, Arnaud Couloux, Xiaopeng Fu, Jérémy Just, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen, ANR-13-BSV7-0014,DODO,Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose(2013), ANR-12-BSV6-0005,AuxiFlo,Couplage entre le réseau transcriptionnel de l'auxine et l'identité florale(2012), ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences(2011), European Project: 341076,EC:FP7:ERC,ERC-2013-ADG,SEXYPARTH(2014), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Équipe 2 - Écologie Végétale et Zones Humides (EVZH), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, GET-PACBIO program (programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE), French National Institute of Agronomic Research (INRA), program Fonds Recherche of Ecole Normale Superieure-Lyon-France, Genoscope, French National Research Agency program DODO : ANR-16CE20-0024-03, French National Research Agency program AUXIFLO : ANR-12-BSV6-0005, Labex Saclay Plant Sciences-SPS : ANR-10- LABX-0040-SPS, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), and Huazhong Agricultural University [Wuhan] (HZAU)
Subjects: 0301 basic medicine, Candidate gene, Genotype, Flowers, Biology, Genes, Plant, Rosa, Genome, Article, Domestication, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Gene Expression Regulation, Plant, Genetic variation, Genetics, rosaceae, Rosa chinensis, Gene, odeur, couleur, Hybrid, Plant Proteins, Vegetal Biology, Whole Genome Sequencing, génome, Genetic Variation, Genomics, Sequence Analysis, DNA, biology.organism_classification, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, gène candidat, Ploidy, séquençage adn, Biologie végétale, Genome, Plant
Abstract: Epub ahead of print; International audience; Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.
Published: 2018

10. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Author: Cristina Vives, Sebastian N. W. Hoernstein, Dennis W. Stevenson, Anders Larsson, Klaus F. X. Mayer, Fabian B. Haas, Jane Grimwood, Priya Ranjan, Lucas Schneider, Yong Zhang, Ralf Reski, Florian Maumus, Stuart F. McDaniel, Michael Tillich, Thomas Widiez, Carl J. Rothfels, Andreas Zimmer, Daniel S. Rokshar, Yasuko Kamisugi, Heidrun Gundlach, Sean W. Graham, Klaas Vandepoele, Richard D. Hayes, Aikaterini Symeonidi, Omar Abu Saleh, Andrew C. Cuming, Jeremy Schmutz, Jordi Morata, Shengqiang Shu, Jérôme Salse, Joerg Fuchs, Ralph S. Quatrano, Daniel Lang, Juan Carlos Villarreal Aguilar, Kristian K. Ullrich, Gerald A. Tuskan, Fay-Wei Li, Mathieu Piednoël, Pierre-François Perroud, Florent Murat, Ann M. Wymore, Gane Ka-Shu Wong, Manuel Hiss, Jerry Jenkins, Lee E. Gunter, Josep M. Casacuberta, Nico van Gessel, Wellington Muchero, Jeremy Phillips, Michiel Van Bel, Eva L. Decker, Rabea Meyberg, Stefan A. Rensing, Guillaume Blanc, Fritz Thümmler, David Goodstein, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), United States Department of Energy, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Helmholtz-Zentrum München (HZM), Center for Research in Agricultural Genomics, Freiburg Initiative in Systems Biology, University of Freiburg [Freiburg], Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), London School of Hygiene and Tropical Medicine (LSHTM), Luleå University of Technology (LUT), BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Department of Biological Sciences [Edmonton], University of Alberta, Wolfgang Pauli Institute (WPI), University of Vienna [Vienna], Department of Molecular Psychiatry, Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Plant Biotechnology, Faculty of Biology, University of Freiburg, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Office of Science of the US Department of Energy [DEAC02-05CH11231], German Research Foundation [DFG RE 837/10-2], Excellence Initiative of the German Federal and State Governments [EXC 294], German Federal Ministry of Education and Research [BMBF FRISYS], US National Science Foundation [IOS339156, IOS-1444490], U.S. National Science Foundation [DBI-0735191, DBI-1265383], UK Biological Sciences and Biotechnology Research Council [BB/F001797/1], Ghent University’s Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project [01MR0410W], Spanish Ministerio de Economıa y Competitividad [AGL2013-43244-R], Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB), EMBO Long-Term Fellowships [ALTF 1166-2011], German Research Foundation [SFB924], German Ministry of Education and Research [BMBF, 031A536/de.NBI], European Project: 267146,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,EMBOCOFUND2010(2011), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum München = German Research Center for Environmental Health, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), European Commission, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), and École normale supérieure - Paris (ENS Paris)
Subjects: 0301 basic medicine, Sequence assembly, Plant Biology, plant, Plant Science, Genome, Gene duplication, chromosome, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, biology, synteny, food and beverages, Single Nucleotide, Biological Evolution, Chromatin, ddc:580, duplication, Evolution, Chromosome, Plant, Moss, Methylation, Duplication, Synteny, Physcomitrella Patens, Physcomitrellapatens, Genome, Plant, Biotechnology, Transposable element, Centromere, Plant Biology & Botany, Physcomitrella patens, Polymorphism, Single Nucleotide, Chromosomes, Plant, Chromosomes, moss, 03 medical and health sciences, Genetic, evolution, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Polymorphism, Gene, genome, Human Genome, Genetic Variation, Cell Biology, DNA Methylation, biology.organism_classification, Bryopsida, Recombination, 030104 developmental biology, Evolutionary biology, DNA Transposable Elements, Biochemistry and Cell Biology, methylation
Abstract: et al., The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes., The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Support to RR and SAR by the German Research Foundation (DFG RE 837/10-2), the Excellence Initiative of the German Federal and State Governments (EXC 294), and by the German Federal Ministry of Education and Research (BMBF FRISYS), is highly appreciated. CoGe is supported by the US National Science Foundation under Award Numbers IOS-339156 and IOS-1444490, CyVerse is supported by the U.S. National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383. YK and ACC are grateful for support from the UK Biological Sciences and Biotechnology Research Council (Grant BB/F001797/1). KV acknowledges the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project (no 01MR0410W) of Ghent University. JC is grateful for support from the Spanish Ministerio de Economía y Competitividad (Grant AGL2013-43244-R). RSQ is grateful to Monsanto (St. Louis, MO, USA) for sequencing genomic DNA of P. patens accession Kaskaskia. The 1000 Plants (1 KP) initiative, led by GKSW, is funded by the Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB). TW was supported by EMBO Long-Term Fellowships (ALTF 1166-2011) and by Marie Curie Actions (European Commission EMBOCOFUND2010, GA-2010-267146). The work conducted at PGSB was supported by the German Research Foundation (SFB924) and German Ministry of Education and Research (BMBF, 031A536/de.NBI).
Published: 2018

11. Epigenetics in forest trees

Author: Régis Fichot, Luc E. Pâques, Jörg Tost, Svetlana Gribkova, Léopoldo Sanchez-Rodriguez, Christophe Ambroise, Grégoire Le-Provost, Vincent Segura, Stéphane Maury, Isabel Allona, Mamadou Dia Sow, Christophe Plomion, Daniel Conde, Jérôme Salse, Véronique Jorge, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Centro de Biotecnologia y Genomica de Plantas (CBGP), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office national des forêts (ONF), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Laboratoire d'Epigénétique et d'Environnement [Evry] (CNG - CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de Genotypage-Institut de Génomique [Evry], Marie Mirouze, Etienne Bucher, and Philippe Gallusc
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Forest management, forest management, Climate change, Context (language use), adaptation, épigenetics, Biology, 01 natural sciences, phenotypic plasticity, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Local adaptation, Phenotypic plasticity, business.industry, Global warming, Environmental resource management, épigenomics, 15. Life on land, 030104 developmental biology, climate change, 13. Climate action, breeding, Tree breeding, Adaptation, business, forest trees, 010606 plant biology & botany
Abstract: International audience; Forest trees are long-lived organisms subject to repeated environmental constraints throughout their long lifetimes. They have developed various mechanisms enabling them to cope with fluctuating environmental conditions during their life span, and to survive to current climate change. Epigenetics has recently emerged as a powerful set of mechanisms regulating various developmental processes, plant growth and responses to environmental variations. Such epigenetic mechanisms, which may remain stable along tree life or across generations, constitute a source of rapid phenotypic variations potentially improving adaptation of the plants in situations in which naturally occurring mutations are very rare.In this review, we summarize recent advances in forest tree epigenomics. We first draw the particularities of trees and the available (epi) genomics resources and strategies. Then, we discuss the potential contributions of epigenetics to cope with global climate change and regulate various developmental processes, such as developmental transitions during the annual cycle, phenotypic plasticity in response to environmental variations and stress memory, as well as local adaptation. Finally, we propose some challenges for forest management and highlighted the need to take epigenetics into account in forest tree breeding strategies.
Published: 2018

12. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements

Author: Zhiwu Quan, Songtao Gui, Liping Shu, Xiaolei Wang, Peng Jing, Qiuju Xia, Zhihua Wu, Yi Ding, Zhixuan Zhu, Wedong Ke, Jérôme Salse, Rui Cao, Hongyuan Zhang, State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Wuhan Ice-Harbor Biological Technology Co, National Natural Science Foundation of China 31271310, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 0301 basic medicine, Genetic Markers, China, Genotype, Genetic Linkage, Karyotype, Plant Science, Chromosomal rearrangement, Computational biology, génome extra chromosomique, Biology, Nelumbo, Genome, Polymorphism, Single Nucleotide, DNA sequencing, Chromosomes, Plant, BioNano optical map, 03 medical and health sciences, nanobiotechnologie, Gene mapping, Genetic linkage, chromosome rearrangement, Centromere, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genetic linkage map, scaffold anchoring, Chromosome, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Nelumbo nucifera, Cell Biology, Genomics, Sequence Analysis, DNA, Plant Breeding, 030104 developmental biology, Genome, Plant, Microsatellite Repeats
Abstract: Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
Published: 2018

13. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

Author: Catherine Feuillet, Raphael Flores, Tzion Fahima, Marco Maccaferri, Delphine Steinbach, Hadi Quesneville, Silvio Salvi, Umar Masood Quraishi, Jérôme Salse, Jaroslav Doležel, Michael Alaux, Beat Keller, Caroline Pont, Hikmet Budak, Séverine Foucrier, Sébastien Guizard, Florent Murat, Yannick Bidet, University of Zurich, Salse, Jérôme, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Plateforme GINA, Université de Clermont, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Departement of Evolutionary and Environmental Biology, University of Haifa [Haifa], Faculty of Engineering and Natural Sciences, Sabanci University [Istanbul], Institut de Biologie des Plantes, Universität Zürich [Zürich] = University of Zurich (UZH), DiSTA- Agronomia, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), DiSTA-Agronomia, INRA (Genetique et Amelioration des Plantes' reference: 'Appel d'Offre AIP Bioressources'), Auvergne region (Pole de competitivite: Cereales Vallee reference: programme 'Semences de Demain'), Agence Nationale de la Recherche (Programs ANRjc-PaleoCereal) [ANR-09-JCJC-0058-01], Agence Nationale de la Recherche (programme ANR Blanc-PAGE) [ANR-2011-BSV6-00801], European 7th Framework Programme (programme 'TRITICEAE GENOME') [FP7-212019], Institute of Experimental Botany, Universität Zürich [Zürich] (UZH), Università di Bologna [Bologna] (UNIBO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Caroline Pont, Florent Murat, Sébastien Guizard, Raphael Flore, Séverine Foucrier, Yannick Bidet, Umar Masood Quraishi, Michael Alaux, Jaroslav Doležel, Tzion Fahima, Hikmet Budak, Beat Keller, Silvio Salvi, Marco Maccaferri, Delphine Steinbach, Catherine Feuillet, Hadi Quesneville, and Jérôme Salse
Subjects: 0106 biological sciences, ble tendre, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Plant Science, 580 Plants (Botany), 01 natural sciences, paléogène, 1307 Cell Biology, 10126 Department of Plant and Microbial Biology, partitioning, 1110 Plant Science, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Conserved Sequence, Triticum, Genes, Dominant, 2. Zero hunger, Genetics, 0303 health sciences, paleogenomic, conserved orthologous set, food and beverages, Genomics, Gene conservation, gène dominant, Genome, Plant, Recombination, Autre (Sciences du Vivant), Genetic Markers, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], DNA, Plant, SNP, Biotechnologies, Plasticity, Biology, dominance, Models, Biological, Polymorphism, Single Nucleotide, Synteny, Chromosomes, Plant, Evolution, Molecular, Polyploidy, 03 medical and health sciences, 1311 Genetics, COS, Gene, 030304 developmental biology, Single nucleotide polymorphisms, Sequence Analysis, DNA, Cell Biology, paleogenomics, évolution chromosomique, 010606 plant biology & botany
Abstract: édition online; Bread wheat derives from a grass ancestor structured in 7 protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing COS (Conserved Orthologous Set) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supradominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat. This article is protected by copyright. All rights reserved.
Published: 2013

14. Wheat paleohistory created asymmetrical genomic evolution

Author: Caroline Pont, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0301 basic medicine, Transposable element, Chromosome number, [SDV]Life Sciences [q-bio], asymmetric synthesis, Adaptation, Biological, Plant Science, Biology, Genome, Diploidization, Evolution, Molecular, Polyploidy, genomic, 03 medical and health sciences, blé, wheat, evolution, Epigenetics, Gene, Triticum, Dominance (genetics), Genetics, food and beverages, Diploidy, 030104 developmental biology, synthèse asymétrique, Ploidy, évolution génomique, Genome, Plant
Abstract: Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes.
Published: 2017

15. Reconstructing the genome of the most recent common ancestor of flowering plants

Author: Christophe Klopp, Alix Armero, Florent Murat, Jérôme Salse, Caroline Pont, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), ANR Blanc-PAGE (ref: ANR-2011-BSV6-00801) et 'Région Auvergne, Allocation de Recherche Territoire, Agriculture, Alimentation, Nutrition et Santé Humaine' (contrat 23000720), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Most recent common ancestor, [SDV]Life Sciences [q-bio], Plant genetics, Genomics, Flowers, Biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Magnoliopsida, Extant taxon, ressource génétique végétale, Genetics, Translational genomics, Eudicots, Gene, Phylogeny, 2. Zero hunger, plants, génome, food and beverages, animal genetic resources, 15. Life on land, plant genetics, 030104 developmental biology, Evolutionary biology, plante à fleurs, Mutation, Genome, Plant, 010606 plant biology & botany
Abstract: We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops. The estimation of the timing of angiosperm evolution, based on MRCA genes, suggested that this group emerged 214 million years ago during the late Triassic era, before the oldest recorded fossil. Finally, the MRCA constitutes a unique resource for scientists to dissect major agronomic traits in translational genomics studies extending from model species to crops.
Published: 2017

16. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Author: Debbie Wong, Abraham B. Korol, Eduard Akhunov, Catherine Feuillet, Gina Brown-Guedira, Ivan Mikoulitch, Jan Dvorak, Martin W. Ganal, Marco Maccaferri, Curtis J. Pozniak, Luigi Cattivelli, Joerg Plieske, Rudi Appels, Rudy Dolferus, Anna M. Mastrangelo, Ming-Cheng Luo, Bevan Emma Huang, Alexandra M. Allen, Jorge Dubcovsky, Matthew K. Morell, Michele Morgante, Cindy Lawley, Shichen Wang, Morten Lillemo, Sara Giulia Milner, Shiaoman Chao, Alex Whan, Alina Akhunova, Kerrie Forrest, Matthew J. Hayden, Gary L A Barker, Keith J. Edwards, Jérôme Salse, Stuart Stephen, Roberto Tuberosa, Colin Cavanagh, Silvio Salvi, Ralf Wieseke, Diane E. Mather, Department of Plant Pathology, Shizuoka University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, USDA-ARS : Agricultural Research Service, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Department of Agricultural Sciences, Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Waite Res Inst, Australian Ctr Plant Funct Genom, University of Adelaide, Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa [Haifa], Integrated Genomics Facility, Kansas State University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine - University of Udine [Italie], Plant Genetics and Bioinformatics, UC Davis Plant Sciences, University of Hradec Kralove, CSIRO Plant Industry, Department of Plant Sciences (DPS), University of Cambridge [UK] (CAM), Illumina, Inc., CSIRO Plant Industrie, Dept Plant Pathol, Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Università di Bologna [Bologna] (UNIBO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), S. Wang, D. Wong, K. Forrest, A. Allen, S. Chao, B. Huang, M. Maccaferri, S. Salvi, S. Milner, L. Cattivelli, A. Mastrangelo, A. Whan, S. Stephen, G. Barker, R. Wieseke, J. Plieske, M. Lillemo, D. Mather, R. Appel, R. Dolferu, G. Brown-Guedira, A. Korol, A. Akhunova, C. w. Feuillet, J. Salse, M. Morgante, C. Pozniak, M. Luo, J. Dvorak, M. Morell, J. u. Dubcovsky, M. Ganal, R. Tuberosa, C. Lawley, I. Mikoulitch, C. Cavanagh, K. Edward, M. Hayden, and E. Akhunov
Subjects: 0106 biological sciences, Technology, SNP ARRAY, LINKAGE DISEQUILIBRIUM, Polyploid wheat, [SDV]Life Sciences [q-bio], Plant Science, Medical and Health Sciences, 01 natural sciences, Genetic diversity, Gene Frequency, single nucleotide polymorphism, Genotype, WIDE ASSOCIATION, Cluster Analysis, ComputingMilieux_MISCELLANEOUS, AEGILOPS-TAUSCHII, POPULATION, Triticum, Research Articles, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, Genome, biology, Chromosome Mapping, food and beverages, Wheat iSelect array, Single Nucleotide, genetic diversity, Biological Sciences, SNP genotyping, DURUM-WHEAT, wheat iSelect array, Genome, Plant, Biotechnology, Genetic Markers, Genotyping, SNP DISCOVERY, Population, Single-nucleotide polymorphism, SEQUENCE, Polymorphism, Single Nucleotide, GENETIC ARCHITECTURE, Polyploidy, polyploid wheat, 03 medical and health sciences, Genetic variation, Aegilops tauschii, Polymorphism, TRITICUM-AESTIVUM L, education, Alleles, 030304 developmental biology, genotyping, high-density map, Genetic Loci, Genetic Variation, High-density map, Plant, biology.organism_classification, Single nucleotide polymorphism, High density map, Evolutionary biology, HEXAPLOWHEAT, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat. © 2014 The Authors Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Published: 2014

17. Identification of glycosyltransferases involved in cell wall synthesis of wheat endosperm

Author: Colette Larré, A. Partier, Dominique Tessier, Caroline Pont, Hélène Rogniaux, J. Marion, Brigitte Bouchet, Mathilde Francin-Allami, Fabienne Guillon, Anne-Laure Chateigner-Boutin, M. Suliman, Jérôme Salse, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut National de la Recherche Agronomique (INRA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), inconnu, Inconnu, Univ Fed Santa Maria, Dept Solos, BR-97105900 Santa Maria, RS, Brazil, and Australia-India Council, CEPIA post-doc
Subjects: Dietary Fiber, Proteomics, 0106 biological sciences, [SDV]Life Sciences [q-bio], 01 natural sciences, Biochemistry, Mass Spectrometry, Endosperm, Cell Wall, Triticum, Plant Proteins, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, MESH: Plant Proteins, Wheat endosperm, food and beverages, Wheat, MESH: Glycosyltransferases, symbols, Cell fractionation, Biophysics, MESH: Triticum, Biology, Polysaccharide, MESH: Endosperm, Cell wall, MESH: Golgi Apparatus, 03 medical and health sciences, symbols.namesake, MESH: Cell Wall, Polysaccharides, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Humans, 030304 developmental biology, MESH: Mass Spectrometry, MESH: Humans, Glycosyltransferases, Golgi apparatus, Fusion protein, MESH: Polysaccharides, chemistry, MESH: Dietary Fiber, Subcellular fraction, Biogenesis, 010606 plant biology & botany
Abstract: International audience; Plant cell walls are complex structures critical for plant fitness and valuable for human nutrition as dietary fiber and for industrial uses such as biofuel production. The cell wall polysaccharides in wheat endosperm consist of two major polymers, arabinoxylans and beta-glucans, as well as other minor components. Most of these polysaccharides are synthesized in the Golgi apparatus but the mechanisms underlying their synthesis have yet to be fully elucidated and only a few of the enzymes involved have been characterized. To identify actors involved in the wheat endosperm cell wall formation, we used a subcellular fractionation strategy to isolate Golgi-enriched fractions from endosperm harvested during active cell wall deposition. The proteins extracted from these Golgi-enriched fractions were analyzed by LC-MS/MS. We report the identification of 1135 proteins among which 64 glycosyltransferases distributed in 17 families. Their potential function in cell wall synthesis is discussed. In addition, we identified 63 glycosylhydrolases, some of which may be involved in cell wall remodeling. Several glycosyltransferases were validated by showing that when expressed as fusion proteins with a fluorescent reporter, they indeed accumulate in the Golgi apparatus. Our results provide new candidates potentially involved in cell wall biogenesis in wheat endosperm.
Published: 2013

18. Deciphering the evolutionary interplay between subgenomes following polyploidy: A paleogenomics approach in grasses

Author: Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Agence Nationale de la Recherche (ANR Blanc-PAGE) ANR-2011-BSV6-00801, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Karyotype, plant evolution, Genomics, Plant Science, Biology, Genome, Polyploidy, 03 medical and health sciences, Common descent, Gene duplication, Genetics, Genome size, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Plant evolution, poaceae, Chromosome, 15. Life on land, Biological Evolution, 030104 developmental biology, grasses, paleogenomics, Evolutionary biology, Genome, Plant
Abstract: International audience; How did plant species emerge from their most recent common ancestors (MRCAs) 250 million years ago? Modern plant genomes help to address such key questions in unveiling precise species genealogies. The field of paleogenomics is undergoing a paradigm shift for investigating species evolution from the study of ancestral genomes from extinct species to deciphering the evolutionary forces (in terms of duplication, fusion, fi ssion, deletion, and translocation) that drove present-day plant diversity (in terms of chromosome/gene number and genome size). In this review, inferred ancestral karyotype genomes are shown to be powerful tools to (1) unravel the past history of extant species by recovering the variations of ancestral genomic compartments and (2) accelerate translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.
Published: 2016

19. Ancestors of modern plant crops

Author: Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Agence Nationale de la Recherche (ANR Blanc-PAGE) ANR-2011-BSV6-00801, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: Crops, Agricultural, 2. Zero hunger, 0301 basic medicine, Comparative genomics, [SDV]Life Sciences [q-bio], fungi, Computational Biology, food and beverages, Genomics, Plant Science, Biology, Biological Evolution, Genome, Magnoliopsida, 03 medical and health sciences, 030104 developmental biology, Common descent, Evolutionary biology, Ancestral genome, State of art, Genome, Plant, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Recent accumulation of plant genomic resources offers the opportunity to compare modern genomes and model their evolutionary history from their reconstructed Most Recent Common Ancestors (MRCAs) that can be used as a guide to unveil the forces driving the evolutionary success of angiosperms and ultimately to perform applied translational research from models to crops. This article reviews the current state of art of recent structural comparative genomics studies through ancestral genome reconstruction, that is, the field of in silico paleogenomics.
Published: 2016

20. Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Author: Hadi Quesneville, Mélanie Molinier, Michael Alaux, Florent Murat, Laura Burlot, Caroline Pont, Maeva Veyssière, Moaine El Baidouri, Raphaël-Gauthier Flores, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), and European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Structural asymmetry, Chromosome number, Physiology, Plant Science, Biology, Genome, Polymorphism, Single Nucleotide, Synteny, 03 medical and health sciences, DNA Transposable Elements, wheat, evolution, origin, Cumulative effect, Triticum, 2. Zero hunger, Genetics, Models, Genetic, food and beverages, Bread, biology.organism_classification, polyploidization, Biological Evolution, Aegilops speltoides, Mutagenesis, Insertional, 030104 developmental biology, Mutation, ancestor, Ploidy, Genome, Plant
Abstract: In Press; The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
Published: 2016

21. Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

Author: Yves Van de Peer, Florent Murat, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dept Plant Biotechnol & Bioinformat, Universiteit Gent = Ghent University (UGENT), Agence Nationale de la Recherche [ANR-09-JCJC-0058-01, ANR-2011-BSV6-00801], Ghent University (Multidisciplinary Research Partnership 'Bioinformatics: from nucleotides to networks'), Interuniversity Attraction Poles Program [IUAP P6/25], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Ghent University [Belgium] (UGENT), and Universiteit Gent = Ghent University [Belgium] (UGENT)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genome evolution, rearrangement, POLYPLOIDY, Genomics, Bacterial genome size, Biology, 01 natural sciences, Genome, DNA sequencing, GENE LOSS, Evolution, Molecular, 03 medical and health sciences, Species Specificity, REVEALS, evolution, Genetics, synteny, duplication, genome, plasticity, TRANSPOSABLE ELEMENTS, ANCESTRAL VERTEBRATE, NONCODING SEQUENCES, DUPLICATION, RECONSTRUCTION, RICE, IDENTIFICATION, Animals, Letters, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Gene Rearrangement, 0303 health sciences, fungi, food and beverages, Chromosome Mapping, Gene rearrangement, Genome project, Plants, Evolutionary biology, Vertebrates, Genome, Plant, 010606 plant biology & botany
Abstract: Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in 1) evolutionary mechanisms (i.e., polyploidization versus diploidization processes), 2) genome conservation (i.e., coding versus noncoding sequence maintenance), and 3) modern genome architecture (i.e., genome organization including repeats expansion versus contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.
Published: 2012

22. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution

Author: Séverine Foucrier, Gilles Charmet, Catherine Feuillet, Gregory Desmaizieres, Michael Abrouk, Alain Murigneux, Umar Masood Quraishi, Jacques Le Gouis, Caroline Pont, Nathalie Rivière, Jérôme Salse, Carole Confolent, Stéphane Lafarge, Laurent Guerreiro, Etienne Paux, and Florent Murat
Subjects: 2. Zero hunger, 0106 biological sciences, Molecular breeding, Genetics, 0303 health sciences, Genome evolution, food and beverages, Locus (genetics), Cell Biology, Plant Science, Vernalization, Quantitative trait locus, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Cellular localization, 030304 developmental biology, 010606 plant biology & botany, Synteny
Abstract: Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.
Published: 2011

23. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics

Author: Catherine Feuillet, Florent Murat, Umar Masood Quraishi, Michael Abrouk, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Quantitative Trait Loci, Computational biology, Biology, Poaceae, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, PALEOGENOMICS, Molecular evolution, Molecular Biology, Gene, CEREALS, 030304 developmental biology, Synteny, 2. Zero hunger, Comparative genomics, Genetics, 0303 health sciences, Chromosome Mapping, Paleontology, Genomics, Gene Annotation, 15. Life on land, Biological Evolution, EVOLUTION, SYNTENY, Identification (biology), Genome, Plant, Orthologous Gene, 010606 plant biology & botany, Information Systems
Abstract: In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.
Published: 2009

24. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

Author: Jean-Marc Aury, Sébastien Duplessis, Joelle Amselem, Célia Michotey, Delphine Steinbach, Christophe Plomion, Catherine Bodénès, Valérie Barbe, Franck Salin, Jean-Charles Leplé, Patrick Wincker, Hélène Bergès, Nicolas Francillonne, Christophe Klopp, Florent Murat, Jérôme Salse, Barbara Estrada-Mairey, Isabelle Le Clainche, Antoine Kremer, Nathalie Boudet, Caroline Belser, Grégoire Le Provost, Thibault Leroy, Aurélie Canaguier, Christophe Boury, François Ehrenmann, Jonathan Mercier, Isabelle Lesur, Stéphanie Fouteau, Francis Martin, Hadi Quesneville, Cécile Guichard, Tina Alaeitabar, Christine Gaspin, Céline Lalanne, Karine Labadie, Arnaud Couloux, Corinne Da Silva, Patricia Faivre-Rampant, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: 0301 basic medicine, genome sequence, [SDV]Life Sciences [q-bio], education, Computational biology, Genome, Quercus robur, 03 medical and health sciences, Quercus, Genetics, Gene, Ecology, Evolution, Behavior and Systematics, Phylogeny, Whole genome sequencing, Contig, biology, Models, Genetic, Molecular Sequence Annotation, Genome project, Sequence Analysis, DNA, biology.organism_classification, Fosmid, 030104 developmental biology, genomic resources, Genome, Plant, Biotechnology, Reference genome
Abstract: International audience; The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
Published: 2015

25. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Author: Jean-Charles Leplé, Céline Noirot, Antoine Kremer, Christian Burban, Hadi Quesneville, Michael Stierschneider, Valérie Léger, Saneyoshi Ueno, Pascal Bento, Corinne Da Silva, François Buscot, Silvia Fluch, Jérôme Bartholomé, Christophe Plomion, Christophe Klopp, Jean-Marc Aury, François Ehrenmann, Isabelle Lesur, Lasse Feldhahn, Joelle Amselem, Céline Lalanne, Florent Murat, Mika T. Tarkka, Jérôme Salse, Caroline Belser, Sylvie Herrmann, Grégoire Le Provost, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Biométrie et Intelligence Artificielle (UBIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Génomique Info (URGI), Austrian Institute of Technology [Vienna] (AIT), Department of Soil Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), German Centre for Integrative Biodiversity Research, Synthetic and Systems Biology Unit [Szeged], Biological Research Centre [Szeged] (BRC), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Biodiversité, Gènes et Communautés, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Helmholtz Centre for Environmental Research (UFZ), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Phénotype, Sequence assembly, UniGene, comparative genomics, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Gene Expression Regulation, Plant, bud phenology, K01 - Foresterie - Considérations générales, genomic features [EN], ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, biology, bourgeon, Chromosome Mapping, Plant Dormancy, Adaptation, Physiological, Quercus petraea, quercus, Quercus robur, Phénologie, Génotype, Genome, Plant, Research Article, Biotechnology, expression des gènes, Genome evolution, Genetic Speciation, education, fagaceae, de novo assembly, Séquence d'ARN, 03 medical and health sciences, oak, séquençage, Gene, 030304 developmental biology, transcriptome, RNA-seq, Comparative genomics, Base Sequence, Transcription génique, Sequence Analysis, RNA, génomique comparative, 15. Life on land, biology.organism_classification, dormance, Evolutionary biology, 010606 plant biology & botany
Abstract: Background Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1331-9) contains supplementary material, which is available to authorized users.
Published: 2015

26. Evidence of intense chromosomal shuffling during conifer evolution

Author: Yoshihiko Tsumura, Christophe Plomion, María-Teresa Cervera, Saneyoshi Ueno, Nuria de María, Jérôme Bartholomé, François Ehrenmann, José-Antonio Cabezas, Yoshinari Moriguchi, Marina de Miguel, Jean Marc Gion, Florent Murat, Kentaro Uchiyama, Hélène Lagraulet, Jérôme Salse, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Niigata University, Department of Forest Genetics, Federal Research and Training Centre for Forests Natural Hazards and Landscape, Université de Tsukuba = University of Tsukuba, and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA)
Subjects: 0106 biological sciences, angiosperme, Letter, [SDV]Life Sciences [q-bio], Évolution, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Cuppressaceae gymnosperm, K01 - Foresterie - Considérations générales, ComputingMilieux_MISCELLANEOUS, Genomic organization, Genetics, 0303 health sciences, biology, F70 - Taxonomie végétale et phytogéographie, Pinaceae, lignée cellulaire, [SDE]Environmental Sciences, Genome evolution, chromosomal rearrangement, Séquence nucléotidique, comparative mapping, Pinaceae synteny, Chromosomal rearrangement, Chromosome, Synteny, 03 medical and health sciences, Cuppressaceae, Angiospermae (799XXXXXXX007), Gymnosperm, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Caryotype, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Génome, Cartographie, Cupressaceae, biology.organism_classification, Gène, gymnosperme, Gymnospermae, 010606 plant biology & botany
Abstract: Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkagemapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma Pinaceae and Cupressaceae.We propose for the first time amodel based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n=12) and Cupressaceae (with n=11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes. ©The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Published: 2015

27. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Author: Kathrin Klee, Wenju Hou, Yang Xia, Erli Pang, Florent Murat, Honghe Sun, Xiang Zhao, Jingan Liu, Yan Zhang, Ying Huang, Ruiqiang Li, Jianguo Zhang, Yunfu Li, Yi Ren, Haiying Zhang, Zequn Zheng, Tao Tan, Linyong Mao, Xiaohua Zou, Yimin Xu, Zhaoliang Zhang, Jiao Jiang, James J. Giovannoni, Qun Hu, Shaogui Guo, Juan Wang, Junyi Wang, Kui Lin, Xinming Liang, Aureliano Bombarely, Yong Xu, Dequan Liang, Mingyun Huang, Tian Lv, Kui Wu, Peixiang Ni, Bangqing Huang, Mingzhu Wu, Silin Zhong, Qinghe Kou, Ye Yin, Guoyi Gong, Miao Xing, Yi Zheng, Byung-Kook Ham, Zhonghua Zhang, Hanhui Kuang, Heiko Schoof, Xingping Zhang, Xiaosen Guo, Jérôme Salse, Hong Zhao, Hongju He, Hongping Yi, Amnon Levi, Xuesong Hu, Shanshan Dong, Zhiwen Wang, Zhangjun Fei, Jiumeng Min, Shan Gao, Lukas A. Mueller, Jun Wang, Bo Wang, Sanwen Huang, William J. Lucas, Natl Engn Res Ctr Vegetables, Key Lab Biol & Genet Improvement Hort Crops N Chi, Beijing Acad Agr & Forestry Sci, Boyce Thompson Inst Plant Res, Cornell University [New York], Beijing Genom Inst Shenzhen, T Life Res, Fudan University [Shanghai], Coll Plant Sci & Technol, China Agricultural University (CAU), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dept Plant Biol, Coll Biol Sci, University of California [Davis] (UC Davis), University of California-University of California, Inst Vegetables & Flowers, Chinese Academy of Agricultural Sciences (CAAS), Coll Life Sci, Beijing Normal University (BNU), Coll Hort & Forestry, Huazhong Agricultural University, Natl Engn Res Ctr Vegetables, Key Lab Biol & Genet Improvement Hort Crops N Chi, Beijing, Inst Nutzpflanzenwissensch & Ressource, Rheinische Friedrich-Wilhelms-Universität Bonn, Xinjiang Acad Agr Sci, Beijing Novogene Bioinformat Technol Co Ltd, Vegetable Lab, United States Department of Agriculture, Robert W Holley Ctr Agr & Hlth, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Ministry of Science and Technology of the People's Republic of China [2010DFB33740, 2012AA020103, 2012AA100101, 2012AA100103, 2012AA100105], Ministry of Agriculture of the People's Republic of China [CARS-26], Major Program of Beijing Natural Science Foundation of China [5100001], Beijing Municipal Science and Technology Commission of China [D111100001311002], National Natural Science Foundation of China [30972015, 31171980, 31272184], Agence Nationale de la Recherche [ANR-09-JCJC-0058-01], USDA National Institute of Food and Agriculture [NIFA 201015479], US National Science Foundation [IOS-0923312, IOS-1025642], US-Israel Binational Agricultural Research and Development Fund [IS-4223-09C], USDA Agricultural Research Service, Boyce Thompson Institute [Ithaca], University of California (UC)-University of California (UC), Huazhong Agricultural University [Wuhan] (HZAU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Cornell University, Beijing Normal University, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Germplasm, EXPRESSION, Citrullus lanatus, [SDV]Life Sciences [q-bio], Genomics, Subspecies, 01 natural sciences, Genome, 03 medical and health sciences, Genetic variation, Botany, Genetics, RNA-SEQ, PLANT, Citrullus, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, biology, IDENTIFICATION, FRUIT, MADS-BOX GENE, respiratory system, biology.organism_classification, DNA-SEQUENCES, EVOLUTION, DISTANCE, TOMATO, human activities, 010606 plant biology & botany
Abstract: Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.
Published: 2013

28. In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

Author: Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Grants from the Agence Nationale de la Recherche (Programs ANRjc-PaleoCereal, ref: ANR-09-JCJC-0058-01 and program ANR Blanc-PAGE, ref: ANR-2011-BSV6-00801), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Genetics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, Scale (ratio), In silico, High resolution, Plant Science, Computational biology, Genomics, Biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Archaeology, Gene, Genome, Plant, 030304 developmental biology, 010606 plant biology & botany
Abstract: Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today.
Published: 2012

29. Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

Author: Caroline Pont, Rongzhi Zhang, Long Mao, Aili Li, Michael Abrouk, Florent Murat, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Inst Crop Sci, Chinese Academy of Agricultural Sciences (CAAS), Agence Nationale de la Recherche [ANR-09-JCJC-0058-01, ANR-2011-BSV6-00801], and Ministry of Science and Technology of China [2009AA02Z307, 2012AA10A308
Subjects: 0106 biological sciences, Transposable element, EXPRESSION, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, MicroRNA Gene, Plant Science, Biology, BIOLOGICAL NETWORKS, Poaceae, 01 natural sciences, Gene dosage, Genome, SEQUENCE, 03 medical and health sciences, Gene duplication, microRNA, TRANSCRIPTION FACTOR, RICE, Gene, LATERAL ROOT DEVELOPMENT, Research Articles, 030304 developmental biology, Genetics, 0303 health sciences, food and beverages, Cell Biology, 15. Life on land, EVOLUTION, MIRNA GENES, MicroRNAs, Evolutionary biology, ARABIDOPSIS-THALIANA, Ploidy, PLANT GENOMES, Genome, Plant, 010606 plant biology & botany
Abstract: The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us to unravel (1) contrasted genome conservation patterns of miRNAs in monocots and eudicots after whole-genome duplication (WGD), (2) an ancestral miRNA founder pool in the monocot genomes dating back to 100 million years ago, (3) miRNA subgenome dominance during the post-WGD diploidization process with selective miRNA deletion complemented with possible transposable element-mediated return flows, and (4) the miRNA/target interaction-directed differential loss/retention of miRNAs following the gene dosage balance rule. Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation.
Published: 2012

30. Comparative mapping in the Fagaceae and beyond with EST-SSRs

Author: Emilie Chancerel, Guy Roussel, Christophe Boury, Claudia Mattioni, Fiorella Villani, Francesca Bagnoli, Christophe Plomion, Antoine Kremer, Pablo G. Goicoechea, Florent Murat, Oliver Gailing, Florian Alberto, Catherine Bodénès, Jerome Durand, Giovanni G. Vendramin, Jérôme Salse, Hans Peter Koelewijn, Carolina Soliani, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology, Georg-August-Universität Göttingen, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Georg-August-University = Georg-August-Universität Göttingen, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Georg-August-University [Göttingen]
Subjects: 0106 biological sciences, carte génétique, Genetic Linkage, Biodiversité et Ecologie, vitis-vinifera l, Inheritance Patterns, Population genetics, Plant Science, 01 natural sciences, Quercus, segregating populations, Genome Size, lcsh:Botany, Gene Order, CE - Molecular Ecology Ecotoxicology and Wildlife Management, Wageningen Environmental Research, Genetics, Expressed Sequence Tags, 0303 health sciences, education.field_of_study, Expressed sequence tag, biology, qtl, Chromosome Mapping, food and beverages, genetic-linkage map, analyse comparative, Comparative mapping, Fagaceae, EST-SSRs, lcsh:QK1-989, Sympatry, Mapping, sequence alignment, quercus-robur l, Microsatellite, Quercus petraea, Genome, Plant, quercus robur, Research Article, marqueur génétique, Population, Karyotype, education, fagaceae, Quantitative trait locus, Synteny, castanea-sativa mill, Chromosomes, Plant, Biodiversity and Ecology, Quercus robur, Evolution, Molecular, 03 medical and health sciences, pcr, Alleles, châtaignier, 030304 developmental biology, Fagacee, consensus map, Genetic Variation, 15. Life on land, microsatellite markers, biology.organism_classification, quantitative trait loci, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, bud burst, 010606 plant biology & botany, Microsatellite Repeats
Abstract: Background Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
Published: 2012

31. Mapping ancestral genomes with massive gene loss: a matrix sandwich problem

Author: Eric Tannier, Haris Gavranović, Jérôme Salse, Cedric Chauve, UNIVERSITY OF SARAJEVO - UNIVERZITET U SARAJEVU, Department of Mathematics [Burnaby] (SFU), Simon Fraser University (SFU.ca), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of Sarajevo, UNIVERZITET U SARAJEVU, Department of Mathematics [Burnaby], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Université Lumière - Lyon 2 (UL2)-Inria Grenoble - Rhône-Alpes
Subjects: Whole genome duplication, 02 engineering and technology, Biochemistry, Genome, INTERVALS, Extant taxon, MESH: Animals, MESH: Angiosperms, MESH: Evolution, Molecular, Mammals, Genetics, 0303 health sciences, Heuristic, Combinatorial optimization problem, Solver, Biological Evolution, Original Papers, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, CONTIGUOUS REGIONS, Statistics and Probability, 0206 medical engineering, MESH: Biological Evolution, Biology, MESH: Mammals, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Animals, Humans, Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria, RECONSTRUCTION, MESH: Genome, Molecular Biology, Gene, 030304 developmental biology, Synteny, COMPLEXITY, MESH: Humans, EVOLUTION, SYNTENY, Evolutionary biology, COMPUTATIONAL METHODS, Evolution and Comparative Genomics, PROPERTY, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 020602 bioinformatics
Abstract: Motivation: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto–monocotyledon whose evolution involved massive gene loss following a whole genome duplication. Results: We propose a mapping approach based on the combinatorial notion of ‘sandwich consecutive ones matrix’, which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content. Availability: Upon request to the authors. Contact: haris.gavranovic@gmail.com; eric.tannier@inria.fr
Published: 2011

32. Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.)

Author: Florent Murat, Catherine Feuillet, Jane L. Ward, Christophe M. Courtin, Zoltán Bedo, Umar Masood Quraishi, Peter R. Shewry, Danuta Boros, Jérôme Salse, Caroline Pont, Luc Saulnier, Jan A. Delcour, François Xavier Oury, Fabienne Guillon, Carole Confolent, Sandrine Balzergue, Kurt Gebruers, Mickael Abrouk, Gilles Charmet, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Natl Ctr Plant & Microbial Metabol, Rothamsted Research, Agricultural Institute [Budapest] (ATK MGI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), European, 6th Framework Program 'HEALTHGRAIN' [FOOD-CT-2005-514008], Agence Nationale de la Recherche [ANR-09-JCJC-0058-01], European program 7th Framework Program 'TRITICEAE GENOME' [FP7-212019], Biotechnology and Biological Sciences Research Council of the UK, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), and Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Dietary Fiber, Candidate gene, QTL, Plant genetics, 01 natural sciences, Linkage Disequilibrium, Chromosome regions, CELL-WALL, Triticum, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Genetics, DAIRY-COWS, 0303 health sciences, Reverse Transcriptase Polymerase Chain Reaction, food and beverages, Chromosome Mapping, General Medicine, Bread, Genomics, CATION-ANION DIFFERENCE, Phenotype, RNA, Plant, WHOLE WHEAT, Brachypodium, Genotype, Quantitative Trait Loci, DIVERSITY SCREEN, Locus (genetics), Quantitative trait locus, Biology, Genes, Plant, Chromosomes, Plant, Candidate genes, 03 medical and health sciences, POPULATION-STRUCTURE, RNA, Messenger, 030304 developmental biology, Comparative genomics, Grain fiber content, Wheat Comparative genomics, business.industry, Gene Expression Profiling, Oryza, Quantitative genetics, biology.organism_classification, Biotechnology, ASSOCIATION ANALYSIS, ARABINOXYLAN FIBER, business, Transcriptome, Edible Grain, Biomarkers, 010606 plant biology & botany, Microsatellite Repeats
Abstract: Grain dietary fiber content in wheat not only affects its end use and technological properties including milling, baking and animal feed but is also of great importance for health benefits. In this study, integration of association genetics (seven detected loci on chromosomes 1B, 3A, 3D, 5B, 6B, 7A, 7B) and meta-QTL (three consensus QTL on chromosomes 1B, 3D and 6B) analyses allowed the identification of seven chromosomal regions underlying grain dietary fiber content in bread wheat. Based either on a diversity panel or on bi-parental populations, we clearly demonstrate that this trait is mainly driven by a major locus located on chromosome 1B associated with a log of p value >13 and a LOD score >8, respectively. In parallel, we identified 73 genes differentially expressed during the grain development and between genotypes with contrasting grain fiber contents. Integration of quantitative genetics and transcriptomic data allowed us to propose a short list of candidate genes that are conserved in the rice, sorghum and Brachypodium chromosome regions orthologous to the seven wheat grain fiber content QTL and that can be considered as major candidate genes for future improvement of the grain dietary fiber content in bread wheat breeding programs.
Published: 2011

33. Microsatellite mapping of Ae. speltoides and map-based comparative analysis of the S, G, and B genomes of Triticeae species

Author: Elena A. Salina, Pierre Sourdille, O. B. Dobrovolskaya, Christiane Boeuf, Michel Bernard, Caroline Pont, Jérôme Salse, Inst Cytol & Genet, Siberian Branch, Russian Acad Sci, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), UMR Diversite & Ecophysiol Cereales, Institut National de la Recherche Agronomique (INRA), Siberian Branch of the Russian Academy of Sciences [129], Ministry of Education and Science of the Russian Federation [P409], Russian Foundation for Basic Research [10-04-01458-a], and the Russian Academy of Sciences [Moscow, Russia] (RAS)
Subjects: Genetic Markers, 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, POLYPLOID WHEAT, AEGILOPS-SPELTOIDES, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Polyploidy, 03 medical and health sciences, DIPLOWHEAT, AESTIVUM L, Genetic linkage, Genetics, Common wheat, Triticeae, RFLP ANALYSIS, Phylogeny, Triticum, 030304 developmental biology, CHROMOSOME STRUCTURE, 0303 health sciences, COMMON WHEAT, Models, Genetic, biology, Chromosome Mapping, food and beverages, LEAF RUST RESISTANCE, BREAD WHEAT, DNA, General Medicine, biology.organism_classification, MOLECULAR LINKAGE MAP, Aegilops speltoides, Genetic Techniques, Genetic marker, Microsatellite, Restriction fragment length polymorphism, Agronomy and Crop Science, Genome, Plant, Microsatellite Repeats, 010606 plant biology & botany, Biotechnology
Abstract: The first microsatellite linkage map of Ae. speltoides Tausch (2n = 2x = 14, SS), which is a wild species with a genome closely related to the B and G genomes of polyploid wheats, was developed based on two F(2) mapping populations using microsatellite (SSR) markers from Ae. speltoides, wheat genomic SSRs (g-SSRs) and EST-derived SSRs. A total of 144 different microsatellite loci were mapped in the Ae. speltoides genome. The transferability of the SSRs markers between the related S, B, and G genomes allowed possible integration of new markers into the T. timopheevii G genome chromosomal maps and map-based comparisons. Thirty-one new microsatellite loci assigned to the genetic framework of the T. timopheevii G genome maps were composed of wheat g-SSR (genomic SSR) markers. Most of the used Ae. speltoides SSRs were mapped onto chromosomes of the G genome supporting a close relationship between the G and S genomes. Comparative microsatellite mapping of the S, B, and G genomes demonstrated colinearity between the chromosomes within homoeologous groups, except for intergenomic T6A(t)S.1G, T4AL.5AL.7BS translocations. A translocation between chromosomes 2 and 6 that is present in the T. aestivum B genome was found in neither Ae. speltoides nor in T. timopheevii. Although the marker order was generally conserved among the B, S, and G genomes, the total length of the Ae. speltoides chromosomal maps and the genetic distances between homoeologous loci located in the proximal regions of the S genome chromosomes were reduced compared with the B, and G genome chromosomes.
Published: 2011

34. Unlocking the barley genome by chromosomal and comparative genomics

Author: Burkhard Steuernagel, Kazuhiro Sato, Marie Kubaláková, Takashi Endo, Hiroaki Sakai, Pete E. Hedley, Mihaela Martis, Jenny Morris, Heidrun Gundlach, Andreas Graner, Nils Stein, Matthias Platzer, Tsuyoshi Tanaka, Klaus F. X. Mayer, Jaroslav Dolezel, Jérôme Salse, Marius Felder, Florent Murat, Uwe Scholz, Robbie Waugh, Pavla Suchánková, Stefan Taudien, Takashi Matsumoto, Hui Liu, Thomas Nussbaumer, Hana Šimková, Takeshi Itoh, Stephan K. Roessner, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Helmholtz-Zentrum München (HZM), Ctr Reg Hana Biotechnol & Agr Res, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Lab Plant Genet, Kyoto University [Kyoto], Tsukuba, Université de Tokyo,Faculté d'Agronomie, Inst Plant Sci & Resources, Kurashiki, Okayama University, Bundesministerium fur Bildung und Forschung [0314000], European Union commission [FP7-212019], Ministry of Education, Youth, and Sports of the Czech Republic, European Regional Development Fund [CZ.1.05/2.1.00/01.0007], Institute of Experimental Botany, Okayama University [Okayama], Helmholtz Zentrum München = German Research Center for Environmental Health, and Kyoto University
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, PSEUDO-RESPONSE-REGULATOR, Sequence analysis, FULL-LENGTH CDNAS, Large-Scale Biology Articles, Centromere, Plant Science, Biology, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Evolution, Molecular, 03 medical and health sciences, TRITICUM-AESTIVUM L, Gene Order, ACETYL-COA CARBOXYLASE, GENE-EXPRESSION, POLYPLOWHEAT, 3-PHOSPHOGLYCERATE KINASE, PHYLOGENETIC ANALYSIS, HOMOEOLOGOUS GROUP-4, CEREAL GENOMICS, Gene, Triticum, 030304 developmental biology, 2. Zero hunger, Comparative genomics, Genetics, Gene Rearrangement, 0303 health sciences, Oryza sativa, Models, Genetic, Chromosome, food and beverages, Hordeum, Oryza, Cell Biology, Genomics, Sequence Analysis, DNA, biology.organism_classification, pseudo-response-regulator, acetyl-coa carboxylase, triticum-aestivum l, full-length cdnas, gene-expression, polyploid wheat, 3-phosphoglycerate kinase, phylogenetic analysis, homoeologous group-4, cereal genomics, Hordeum vulgare, Brachypodium distachyon, Genome, Plant, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign; similar to 86% of the estimated; similar to 32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
Published: 2011

35. Palaeogenomics in cereals: Modeling of ancestors for modern species improvement

Author: Catherine Feuillet, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), ANR-09-JCJC-0058-01, ANR-05-BLANC-0258-01, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Duplication, Speciation, Plant genetics, Genomics, Biology, Genes, Plant, Chromosome, 01 natural sciences, Genome, Synteny, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Plant, Polyploidy, 03 medical and health sciences, DUPLICATIONS, Gene duplication, Ancestral genome, RECONSTRUCTION, RICE, Molecular Biology, History, Ancient, 030304 developmental biology, 2. Zero hunger, Markers, 0303 health sciences, General Immunology and Microbiology, Paleontology, food and beverages, Agriculture, General Medicine, Gene Annotation, 15. Life on land, PROVIDE, EVOLUTION, INSIGHTS, Evolutionary biology, Identification (biology), General Agricultural and Biological Sciences, Edible Grain, 010606 plant biology & botany
Abstract: During the last decade, technological improvements led to the development of large sets of plant genomic resources permitting the emergence of high-resolution comparative genomic studies. Synteny-based identification of seven shared duplications in cereals led to the modeling of a common ancestral genome structure of 33.6 Mb structured in five protochromosomes containing 9138 protogenes and provided new insights into the evolution of cereal genomes from their extinct ancestors. Recent palaeogenomic data indicate that whole genome duplications were a driving force in the evolutionary success of cereals over the last 50 to 70 millions years. Finally, detailed synteny and duplication relationships led to an improved representation of cereal genomes in concentric circles, thus providing a new reference tool for improved gene annotation and cross-genome markers development. (C) 2011 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.
Published: 2011

36. Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L

Author: Florent Murat, Hervé Houtin, Vincent Savois, Jean Potier, Grégoire Aubert, Judith Burstin, Marie Georgette Nicolas, Amandine Bordat, Michael Bourgeois, Aurélie Chauveau, Céline Rond, Pascal Marget, Jérôme Salse, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), FP6 EU project 'Grain Legumes Integrated Project' FOOD-CT-2004-506223, GLIP, French national programs Genoplante GOP-PEAC2, GOP-PEAC2, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0106 biological sciences, translational genomics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Genome evolution, functional consensus map, In silico, translational genomic, Biology, CARTOGRAPHIE GENETIQUE, 01 natural sciences, Genome, 03 medical and health sciences, Genetics, Molecular Biology, Gene, Genetics (clinical), pisum sativum, 030304 developmental biology, Synteny, model legume specie, 2. Zero hunger, Investigation, 0303 health sciences, fungi, synteny, food and beverages, model legume species, Phenotypic trait, Genetic marker, 010606 plant biology & botany
Abstract: To identify genes involved in phenotypic traits, translational genomics from highly characterized model plants to poorly characterized crop plants provides a valuable source of markers to saturate a zone of interest as well as functionally characterized candidate genes. In this paper, an integrated view of the pea genetic map was developed. A series of gene markers were mapped and their best reciprocal homologs were identified on M. truncatula, L. japonicus, soybean, and poplar pseudomolecules. Based on the syntenic relationships uncovered between pea and M. truncatula, 5460 pea Unigenes were tentatively placed on the consensus map. A new bioinformatics tool, http://www.thelegumeportal.net/pea_mtr_translational_toolkit, was developed that allows, for any gene sequence, to search its putative position on the pea consensus map and hence to search for candidate genes among neighboring Unigenes. As an example, a promising candidate gene for the hypernodulation mutation nod3 in pea was proposed based on the map position of the likely homolog of Pub1, a M. truncatula gene involved in nodulation regulation. A broader view of pea genome evolution was obtained by revealing syntenic relationships between pea and sequenced genomes. Blocks of synteny were identified which gave new insights into the evolution of chromosome structure in Papillionoids and Eudicots. The power of the translational genomics approach was underlined.
Published: 2011

37. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

Author: Jian-Hong Xu, Florent Murat, Nicolas Guilhot, Jérôme Salse, Eric Tannier, Caroline Pont, Michael Abrouk, Joachim Messing, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), The Plant Genome Initiative at Rutgers (PGIR), Rutgers University [Camden], Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche [ANR-09-JCJC-0058-01], Cogebi [ANR-08-GENM-036-01], Selman A. Waksman Chair in Molecular Genetics, Rutgers University, Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL)
Subjects: 0106 biological sciences, MESH: Genome, Plant, COMPARATIVE MAP, MESH: Zea mays, 01 natural sciences, Genome, CENTROMERE, MESH: Sorghum, DUPLICATIONS, POLYPLOWHEAT, MESH: Chromosomes, Plant, MESH: Phylogeny, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, Recombination, Genetic, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, CHROMOSOME EVOLUTION, food and beverages, Karyotype, MESH: Synteny, MESH: Oryza sativa, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Brachypodium, MESH: Recombination, Genetic, Genome, Plant, Genome evolution, Genetic Speciation, Genomics, ORGANIZATION, Biology, Poaceae, Models, Biological, Synteny, Zea mays, SEQUENCE, Chromosomes, Plant, Evolution, Molecular, 03 medical and health sciences, MESH: Poaceae, Phylogenetics, RICE, Sorghum, 030304 developmental biology, MESH: Genetic Speciation, MAIZE GENOME, Research, MESH: Models, Biological, Oryza, biology.organism_classification, GENE, MESH: Brachypodium, MESH: Karyotyping, Karyotyping, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract: The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5–12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.
Published: 2010

38. Palaeogenomics of plants: synteny-based modelling of extinct ancestors

Author: Eric Tannier, Thomas Faraut, Catherine Feuillet, Joachim Messing, Jérôme Salse, Caroline Pont, Richard Cooke, Florent Murat, Scott A. Jackson, Michael Abrouk, Christophe Plomion, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), The Plant Genome Initiative at Rutgers (PGIR), Rutgers University, Purdue University [West Lafayette], Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Rutgers University [Camden], Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL)
Subjects: 0106 biological sciences, MESH: Genome, Plant, MESH: Plants, Genomics, MESH: Biological Evolution, Plant Science, 01 natural sciences, Genome, Polyploidy, 03 medical and health sciences, Gene mapping, Common descent, Phylogenetics, MESH: Polyploidy, Animals, Humans, MESH: Animals, MESH: Phylogeny, Phylogeny, 030304 developmental biology, Synteny, palaeogenomic, Genetics, 0303 health sciences, MESH: Humans, biology, MESH: Genomics, fungi, food and beverages, Gene Annotation, 15. Life on land, Plants, genomic resource, biology.organism_classification, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Evolutionary biology, Flowering plant, genetic mapping, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Plant, 010606 plant biology & botany
Abstract: Chantier qualité GA; International audience; In the past ten years, international initiatives have led to the development of large sets of genomic resources that allow comparative genomic studies between plant genomes at a high level of resolution. Comparison of map-based genomic sequences revealed shared intra-genomic duplications, providing new insights into the evolution of flowering plant genomes from common ancestors. Plant genomes can be presented as concentric circles, providing a new reference for plant chromosome evolutionary relationships and an efficient tool for gene annotation and cross-genome markers development. Recent palaeogenomic data demonstrate that whole-genome duplications have provided a motor for the evolutionary success of flowering plants over the last 50-70 million years.
Published: 2010

39. The genome of Theobroma cacao

Author: Zi Shi, Thierry Legavre, Jean-Marc Aury, Joseph Moroh Akaza, Jetty S.S. Ammiraju, Claire Lanaud, Ronan Rivallan, Olivier Panaud, Spencer Brown, Valentin Guignon, Stéphanie Bocs, Jose Fernandes Barbosa-Neto, Zhaorong Ma, Xiang Song, Ismael S. Kébé, Christopher Viot, Melissa Kramer, Jérôme Gouzy, Aurélie Bérard, John E. Carlson, Florent Murat, Manuel Ruiz, Didier Clément, François Sabot, Bertrand Pitollat, Dominique Brunel, Michel Boccara, W. Richard McCombie, Xavier Sabau, Stephan C. Schuster, Francis Quetier, Gaëtan Droc, Yufan Zhang, Thomas Schiex, Anne Dievart, Karina Peres Gramacho, Julie Poulain, Wolfgang Golser, Mickael Bourge, Mark J. Guiltinan, Yolande Roguet, Rod A. Wing, Cristian Chaparro, Olivier Fouet, Xavier Argout, Siela N. Maximova, Jérôme Salse, Michael J. Axtell, Pierre Costet, Mathias Tahi, Dave Kudrna, Emmanuel Guiderdoni, Erika Sallet, Laura Gelley, Ange-Marie Risterucci, Diógenes Infante, Patrick Wincker, Mathilde Allègre, Michael Abrouk, Maguy Rodier-Goud, Angélique D'Hont, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Cold Spring Harbor Laboratory (CSHL), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Etude du Polymorphisme des Génomes Végétaux (EPGV), Animalerie spécialisée, Université Bordeaux Segalen - Bordeaux 2, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, MESH: Genome, Plant, Theobroma, MESH: Cacao, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, MESH: Genotype, Gene Expression Regulation, Plant, MESH: Genes, Plant, cocoa statistics, MESH: Models, Genetic, MESH: Evolution, Molecular, In Situ Hybridization, 2. Zero hunger, Genetics, cacaoyer, 0303 health sciences, biology, Homozygote, MESH: DNA, F70 - Taxonomie végétale et phytogéographie, Cacao tree, MESH: DNA Transposable Elements, Genome, Plant, MESH: Homozygote, MESH: Cell Nucleus, Genotype, Quantitative Trait Loci, Moniliophthora, Genes, Plant, Evolution, Molecular, 03 medical and health sciences, MESH: In Situ Hybridization, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Theobroma cacao, MESH: Gene Expression Regulation, Plant, Genome size, Gene, 030304 developmental biology, Cell Nucleus, Cacao, Models, Genetic, Chromosome, DNA, biology.organism_classification, MESH: Quantitative Trait Loci, DNA Transposable Elements, cacao genome, 010606 plant biology & botany
Abstract: International audience; We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
Published: 2010

40. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces

Author: Bikram S. Gill, Michael O. Pumphrey, Dominique Brunel, Thomas Wicker, Frédéric Choulet, James Breen, Marie-Christine Le Paslier, Rudi Appels, Hikmet Budak, Sixin Liu, Jérôme Salse, James A. Anderson, Jizeng Jia, Etienne Paux, Xiuying Kong, Stéphane Schlub, Catherine Gonthier, Beat Keller, Philippe Leroy, Camille Rustenholz, Marta Gut, Arnaud Couloux, Ghislaine Magdelenat, Catherine Feuillet, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Etude du Polymorphisme des Génomes Végétaux, Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Engineering and Natural Sciences, Biological Science and Bioengineering Program, Sabanci University [Istanbul], Centre for Comparative Genomics, Murdoch University, Department of Plant Pathology, Wheat Genetic and Genomic Resources Center, Kansas State University, Department of Agronomy and Plant Genetics, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat a l'Energie Atomique-Genoscope AP2008, Agence Nationale de la Recherche ANR-GPLA06001G, Institut National de la Recherche Agronomique, Turkish Academy of Sciences, Swiss National Science Foundation 105620, University of Zurich, Feuillet, C, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Universität Zürich [Zürich] (UZH), and University of Minnesota [Twin Cities]
Subjects: 0106 biological sciences, Chromosomes, Artificial, Bacterial, ble tendre, Plant Science, 580 Plants (Botany), 01 natural sciences, Genome, 1307 Cell Biology, Contig Mapping, 10126 Department of Plant and Microbial Biology, Gene Duplication, Gene duplication, Génétique des plantes, 1110 Plant Science, Triticeae, Research Articles, 2. Zero hunger, Genetics, 0303 health sciences, Contig, food and beverages, Telomere, Multigene Family, Genome, Plant, Transposable element, DNA, Plant, Sequence analysis, Molecular Sequence Data, Biology, Plants genetics, Genes, Plant, Chromosomes, Plant, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, blé, Gene density, séquençage, triticum aestivum, Gene, 030304 developmental biology, In This Issue, triticum, gène, génome, Sequence Analysis, DNA, Cell Biology, biology.organism_classification, DNA Transposable Elements, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
Published: 2010

41. Fine mapping approaches of two major QTLs for yield in durum wheat

Author: Marta Graziani, Catherine Feuillet, Roberto Tuberosa, A. Demontis, Jérôme Salse, Marco Maccaferri, Università di Bologna [Bologna] (UNIBO), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Società Produttori Sementi (PSB), and Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO)
Subjects: 0106 biological sciences, 0303 health sciences, Yield (engineering), quantitative trait loci (QTL), grain yield, durum wheat, Bioengineering, General Medicine, Biology, 01 natural sciences, Applied Microbiology and Biotechnology, 03 medical and health sciences, Agronomy, 010608 biotechnology, fine mapping, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Grain yield, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Biotechnology
Abstract: absent
Published: 2010

42. The 'inner circle' of the cereal genomes

Author: Catherine Feuillet, Michael Abrouk, Nils Stein, Jérôme Salse, Stéphanie Bolot, Joachim Messing, Umar Masood Masood-Quraishi, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Waksman Institute, PGIR, Rutgers, The State University of New Jersey [New Brunswick] (RU), and Rutgers University System (Rutgers)-Rutgers University System (Rutgers)
Subjects: 2. Zero hunger, 0106 biological sciences, Genetics, 0303 health sciences, Genetic Linkage, food and beverages, Plant Science, Biology, GENETIQUE, Poaceae, Genome structure, Plant biology, 01 natural sciences, Genome, Chromosomes, Plant, DNA sequencing, Evolution, Molecular, 03 medical and health sciences, Genetic marker, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome, Plant, 030304 developmental biology, 010606 plant biology & botany, Synteny
Abstract: Early marker-based macrocolinearity studies between the grass genomes led to arranging their chromosomes into concentric 'crop circles' of synteny blocks that initially consisted of 30 rice-independent linkage groups representing the ancestral cereal genome structure. Recently, increased marker density and genome sequencing of several cereal genomes allowed the characterization of intragenomic duplications and their integration with intergenomic colinearity data to identify paleo-duplications and propose a model for the evolution of the grass genomes from a common ancestor. On the basis of these data an 'inner circle' comprising five ancestral chromosomes was defined providing a new reference for the grass chromosomes and new insights into their ancestral relationships and origin, as well as an efficient tool to design cross-genome markers for genetic studies.
Published: 2009

43. Structure and expression analysis of rice paleo duplications

Author: Peter M. Rogowsky, Xavier Sarda, Umar Masood Quraishi, Stéphanie Bolot, Pascual Perez, Gilles Charmet, Philippe Lessard, Mickael Bosio, Jérôme Salse, Caroline Pont, Mickael Throude, Alain Ghesquiere, Fabienne Bourgis, Alain Murigneux, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), BIOGEMMA, Institut de Recherche pour le Développement (IRD), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, expression génique, Sequence alignment, Paralogous Gene, Biology, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, RIZ, GENETIQUE, évolution moléculaire, Gene Expression Regulation, Plant, Gene Duplication, polyploïdie, Gene duplication, Genetics, Gene family, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Gene, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, 0303 health sciences, Concerted evolution, duplication génique, gène, génome, Gene Expression Profiling, food and beverages, Oryza, Genomics, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Gene expression profiling, oryza sativa, Sequence Alignment, Genome, Plant, 010606 plant biology & botany
Abstract: Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.
Published: 2009

44. Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection

Author: Stéphanie Bolot, Michael Abrouk, Umar Masood Quraishi, Nicolas Guilhot, Mickael Throude, Fernanda Bortolini, Gilles Charmet, Caroline Pont, Alain Murigneux, Sébastien Praud, Jérôme Salse, Carole Confolent, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, Genetic Markers, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Genotype, Quantitative Trait Loci, Genomics, Biology, Quantitative trait locus, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, Conserved sequence, 03 medical and health sciences, Gene mapping, Genetics, Triticum, 030304 developmental biology, Synteny, 2. Zero hunger, Comparative genomics, Expressed Sequence Tags, 0303 health sciences, Base Sequence, LOCUS DES CARACTERES QUANTITATIFS, food and beverages, Oryza, General Medicine, GENETIQUE, Phenotype, Edible Grain, Genome, Plant, Software, 010606 plant biology & botany
Abstract: Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice-wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.
Published: 2009

45. Comparative genomics in the triticeae

Author: Catherine Feuillet, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, 2. Zero hunger, Comparative genomics, 0303 health sciences, [SDV]Life Sciences [q-bio], food and beverages, Quantitative trait locus, Biology, Sorghum, biology.organism_classification, 01 natural sciences, Genome, 03 medical and health sciences, Genetic marker, Evolutionary biology, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ploidy, Triticeae, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; The genomes of grasses are very different in terms of size, ploidy level and chromosome number. Among them, the Triticeae species (wheat, barley, rye) have some of the largest and complex genomes. Comparative mapping studies between rice, maize, sorghum, barley and wheat have pioneered the field of plant comparative genomics a decade ago. They showed that the linear order (colinearity) of genetic markers and genes is very well conserved opening the way to accelerated map-based cloning and defining rice as a model for grasses. More recently, the availability of BAC libraries and large sets of genomic sequences including the completion of the rice genome have permitted micro-colinearity studies that revealed rearrangements between the grass genomes and provided some insights into mechanisms that have shaped their genome during evolution. This review summarizes a decade of comparative genomics Studies In grasses with a special emphasis on the wheat and barley genomes.
Published: 2009

46. Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

Author: Mathias Lorieux, E. Tailliez, Alain Ghesquière, Fabienne Bourgis, Michel Delseny, Isabelle Amabile, Romain Guyot, Hassen Gherbi, Jérôme Salse, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Centre IRD de Montpellier, Institut de Recherche pour le Développement (IRD), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, Asia, Chromatography, Gas, Genotype, Population, Molecular Sequence Data, Locus (genetics), Genes, Plant, 01 natural sciences, Japonica, 03 medical and health sciences, Sequence Homology, Nucleic Acid, Botany, Genetic variation, Genetics, Grain quality, education, Promoter Regions, Genetic, Alleles, 030304 developmental biology, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Genetic diversity, education.field_of_study, Original Paper, Oryza sativa, biology, Base Sequence, food and beverages, Chromosome Mapping, Genetic Variation, Oryza, General Medicine, Sequence Analysis, DNA, biology.organism_classification, Major gene, Phenotype, RIZ PARFUME, Agronomy and Crop Science, RIZ, FRAGANCE, 010606 plant biology & botany, Biotechnology
Abstract: In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93-11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93-11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity.
Published: 2008

47. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis

Author: Philippe Leroy, Catherine Feuillet, Fabrice Legeai, Pierre Sourdille, Jérôme Salse, Anne-Françoise Adam-Blondon, Michael Alaux, Nicolas Guilhot, Etienne Paux, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Université de Rennes (UNIV-RENNES)-Inria Rennes – Bretagne Atlantique
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Chromosomes, Artificial, Bacterial, In silico, Genomics, ANCHORING, Computational biology, Minisatellite Repeats, SOFTWARE, Biology, 01 natural sciences, Genome, PERL SCRIPT, DNA sequencing, Chromosomes, 03 medical and health sciences, Contig Mapping, Chromosome (genetic algorithm), CARTOGRAPHIE PHYSIQUE DU GENOME, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Comparative genomics, PHYSICAL MAPPING, 0303 health sciences, Bacterial artificial chromosome, Contig, COMPLEX GENOMES, Computational Biology, Reproducibility of Results, food and beverages, General Medicine, GENETIQUE, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany, BAC POOLS
Abstract: International audience; Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes.
Published: 2008

48. Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species

Author: Arnaud Bellec, Pierre Sourdille, Philippe Leroy, Jérôme Salse, Carole Dossat, Jean Weissenbach, Bastien Laubin, Ivan Dubois, Michel Bernard, Laurence Cattolico, Marie-Françoise Gautier, Nathalie Chantret, Philippe Joudrier, Michel Caboche, Sébastien Aubourg, François Sabot, Michel Beckert, Boulos Chalhoub, Diversité et adaptation des plantes cultivées (UMR DIAPC), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), UMR 1097 Diversité et Adaptation des Plantes Cultivées, Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-MontpellierSupAgro (MontpellierSupAgro)-Génétique et amélioration des plantes (G.A.P.)-Diversité et Adaptation des Plantes Cultivées (DIA-PC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: 0106 biological sciences, Chromosomes, Artificial, Bacterial, Molecular Sequence Data, Locus (genetics), Biology, CARTOGRAPHIE GENETIQUE, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Genetics, Coding region, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Codon, Molecular clock, Molecular Biology, Gene, Conserved Sequence, Triticum, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, Comparative genomics, 0303 health sciences, Base Sequence, food and beverages, Hordeum, Oryza, Introns, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], DNA, Intergenic, RIZ, 010606 plant biology & botany
Abstract: UMR DIAPC, UMR DAP équipe DGB; We study here the evolution of genes located in the same physical locus using the recently sequenced Ha locus in seven wheat genomes in diploid, tetraploid, and hexaploid species and compared them with barley and rice orthologous regions. We investigated both the conservation of microcolinearity and the molecular evolution of genes, including coding and noncoding sequences. Microcolinearity is restricted to two groups of genes (Unknown gene-2, VAMP, BGGP, Gsp-1, and Unknown gene-8 surrounded by several copies of ATPase), almost conserved in rice and barley, but in a different relative position. Highly conserved genes between wheat and rice run along with genes harboring different copy numbers and highly variable sequences between close wheat genomes. The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases
Published: 2008

49. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Author: Kellye Eversole, Michel Bernard, Daryl Somers, Catherine Feuillet, Jaroslav Dolezel, Michael Alaux, Sonia Vautrin, Philippe Leroy, Monika Michalak, Abraham B. Korol, Hélène Bergès, Andrzej Kilian, Evans Lagudah, Etienne Paux, Frédéric Choulet, Hana Šimková, Wolfgang Spielmeyer, Rudi Appels, Cyrille Saintenac, Pierre Sourdille, Jan Safar, Shahryar F. Kianian, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Evolution, University of Haifa [Haifa], Department of Plant Sciences, North Dakota State University (NDSU), Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Cereal Research Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), International Wheat Genome Sequencing Consortium, Eversole Associates, Centre for Comparative Genomics, Murdoch University, Laboratory of Molecular Cytogenetics and Cytometry, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Experimental Botany of the ASCR, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Agriculture and Agri-Food (AAFC)
Subjects: 0106 biological sciences, Chromosomes, Artificial, Bacterial, Population, BACTERIE, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Crop species, Physical Maps, 01 natural sciences, Genome, Chromosomes, Plant, Polyploidy, Contig Mapping, 03 medical and health sciences, Polyploid, education, Triticum, Gene Library, 030304 developmental biology, Expressed Sequence Tags, 2. Zero hunger, Genetics, Radiation Hybrid Mapping, 0303 health sciences, Bacterial artificial chromosome, education.field_of_study, Polymorphism, Genetic, Multidisciplinary, Contig, Chromosome, food and beverages, Oryza, Bread, Physical Chromosome Mapping, DNA Fingerprinting, GENOMIQUE, CHROMOSOME ARTIFICIEL, Genome, Plant, Microsatellite Repeats, 010606 plant biology & botany
Abstract: As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17–billion–base-pair hexaploid bread wheat genome (2 n = 6 x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)–based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
Published: 2008

50. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution

Author: Richard Cooke, Catherine Feuillet, Stéphanie Bolot, Benoît Piégu, Thomas Calcagno, Jérôme Salse, Michel Delseny, Vincent Jouffe, Michaël Throude, Umar Masood Quraishi, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, Genome evolution, Plant genetics, Plant Science, Biology, 01 natural sciences, Genome, Chromosomes, Plant, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Species Specificity, Phylogenetics, Gene Duplication, Sequence Homology, Nucleic Acid, Gene duplication, Research Articles, Phylogeny, Triticum, 030304 developmental biology, Segmental duplication, 2. Zero hunger, Comparative genomics, Genetics, 0303 health sciences, Oryza sativa, Models, Genetic, food and beverages, Oryza, Cell Biology, GENETIQUE, Sequence Alignment, Genome, Plant, RIZ, 010606 plant biology & botany
Abstract: The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
Published: 2008

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