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98 results on '"Jérôme Salse"'

1. Genomic data integration tutorial, a plant case study

Author: Emile Mardoc, Mamadou Dia Sow, Sébastien Déjean, and Jérôme Salse
Subjects: Omics, Integration, System, Biology, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background The ongoing evolution of the Next Generation Sequencing (NGS) technologies has led to the production of genomic data on a massive scale. While tools for genomic data integration and analysis are becoming increasingly available, the conceptual and analytical complexities still represent a great challenge in many biological contexts. Results To address this issue, we describe a six-steps tutorial for the best practices in genomic data integration, consisting of (1) designing a data matrix; (2) formulating a specific biological question toward data description, selection and prediction; (3) selecting a tool adapted to the targeted questions; (4) preprocessing of the data; (5) conducting preliminary analysis, and finally (6) executing genomic data integration. Conclusion The tutorial has been tested and demonstrated on publicly available genomic data generated from poplar (Populus L.), a woody plant model. We also developed a new graphical output for the unsupervised multi-block analysis, cimDiablo_v2, available at https://forgemia.inra.fr/umr-gdec/omics-integration-on-poplar , and allowing the selection of master drivers in genomic data variation and interplay.
Published: 2024
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2. Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat

Author: Meriem Banouh, David Armisen, Annaig Bouguennec, Cécile Huneau, Mamadou Dia Sow, Caroline Pont, Jérôme Salse, and Peter Civáň
Subjects: RNA-seq, Whole-genome duplication, Genomic shock, Transposable elements, Leaves, Grain, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) less than 10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. The scale of the consequences of polyploidization, and their mechanism of establishment, remain uncertain. Results Here we sampled several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect any massive reprogramming in gene expression, with only around 1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of this differential expression is located on the D subgenome, without consistency in the direction of the expression change. Homoeolog expression bias in synthetic wheat is similar to the pattern observed in the parents. Both differential expression and homoeolog bias are tissue-specific. While up to three families of transposable elements became upregulated in wheat synthetics, their position and distance are not significantly associated with expression changes in proximal genes. Discussion While only a few genes change their expression pattern after polyploidization, they can be involved in agronomically important pathways. Alternative parental combinations can lead to opposite changes on the same subset of D-located genes, which is relevant for harnessing new diversity in wheat breeding. Tissue specificity of the polyploidization-triggered expression changes indicates the remodelling of transcriptomes in synthetic wheat is plastic and likely caused by regulome interactions rather than permanent changes. We discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal. Conclusions Transcriptomic response to polyploidization in synthetic AABBDD wheat is modest and much lower than some previous estimates. Homoeolog expression bias in wheat allohexaploids is mostly attributed to parental legacy, with polyploidy having a mild balancing effect.
Published: 2023
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3. Population genomics of apricots unravels domestication history and adaptive events

Author: Alexis Groppi, Shuo Liu, Amandine Cornille, Stéphane Decroocq, Quynh Trang Bui, David Tricon, Corinne Cruaud, Sandrine Arribat, Caroline Belser, William Marande, Jérôme Salse, Cécile Huneau, Nathalie Rodde, Wassim Rhalloussi, Stéphane Cauet, Benjamin Istace, Erwan Denis, Sébastien Carrère, Jean-Marc Audergon, Guillaume Roch, Patrick Lambert, Tetyana Zhebentyayeva, Wei-Sheng Liu, Olivier Bouchez, Céline Lopez-Roques, Rémy-Félix Serre, Robert Debuchy, Joseph Tran, Patrick Wincker, Xilong Chen, Pierre Pétriacq, Aurélien Barre, Macha Nikolski, Jean-Marc Aury, Albert Glenn Abbott, Tatiana Giraud, and Véronique Decroocq
Subjects: Science
Abstract: 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
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4. Episodes of gene flow and selection during the evolutionary history of domesticated barley

Author: Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse, and Terence A. Brown
Subjects: Barley, Exome sequences, Fertile Crescent, Hordeum vulgare, Gene flow, Origins of agriculture, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Barley 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. Results We 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. Conclusions Identification 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
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5. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author: Bárbara Hufnagel, André Marques, Alexandre Soriano, Laurence Marquès, Fanchon Divol, Patrick Doumas, Erika Sallet, Davide Mancinotti, Sébastien Carrere, William Marande, Sandrine Arribat, Jean Keller, Cécile Huneau, Thomas Blein, Delphine Aimé, Malika Laguerre, Jemma Taylor, Veit Schubert, Matthew Nelson, Fernando Geu-Flores, Martin Crespi, Karine Gallardo, Pierre-Marc Delaux, Jérôme Salse, Hélène Bergès, Romain Guyot, Jérôme Gouzy, and Benjamin Péret
Subjects: Science
Abstract: 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
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6. A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

Author: Bagdevi Mishra, Bartosz Ulaszewski, Joanna Meger, Jean-Marc Aury, Catherine Bodénès, Isabelle Lesur-Kupin, Markus Pfenninger, Corinne Da Silva, Deepak K Gupta, Erwan Guichoux, Katrin Heer, Céline Lalanne, Karine Labadie, Lars Opgenoorth, Sebastian Ploch, Grégoire Le Provost, Jérôme Salse, Ivan Scotti, Stefan Wötzel, Christophe Plomion, Jaroslaw Burczyk, and Marco Thines
Subjects: chromosomes, Fagaceae, genome architecture, genomics, Hi-C, repeat elements, Genetics, QH426-470
Abstract: The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Published: 2022
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7. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Author: Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert, Philippe Leroy, Nicolas Guilhot, Jérôme Salse, Catherine Feuillet, International Wheat Genome Sequencing Consortium, Etienne Paux, Kellye Eversole, Anne-Françoise Adam-Blondon, and Hadi Quesneville
Subjects: Data integration, Information system, Big data, Wheat genomics, genetics and phenomics, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
Published: 2018
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8. Paleogenomics in Triticeae for translational research

Author: Florent Murat, Caroline Pont, and Jérôme Salse
Subjects: Triticeae, Synteny, Duplication, Evolution, Genome, Ancestor, Botany, QK1-989
Abstract: Recent access to Triticeae genome sequences as well as high resolution gene-based genetic maps recently offered the opportunity to compare modern Triticeae genomes and model their evolutionary history from their reconstructed founder ancestors. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day Triticeae and allowed to gain insight into how wheat, barley, rye genomes are organized today compared to their grass relatives (rice, sorghum, millet and maize).
Published: 2014
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9. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

Author: Tao Shi, Cécile Huneau, Yue Zhang, Yan Li, Jinming Chen, Jérôme Salse, Qingfeng Wang, Cas key laboratory of aquatic botany and Watershed ecology, Chinese Academy of Sciences [Beijing] (CAS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), University of Chinese Academy of Sciences, Beijing, China, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China, 32170240-National Natural Science Foundation of China, 31870208-National Natural Science Foundation of China, 2019335-Youth Innovation Promotion Association of the Chinese Academy of Sciences, I-SITE CAP 2025-00002146 SRESRI 2015, Plant2Pro -0001455, 31570220-National Natural Science Foundation of China, and Chinese Academy of Sciences-XDB31000000
Subjects: Magnoliopsida, Acorus, [SDV]Life Sciences [q-bio], Plant Science, Poaceae, Phylogeny
Abstract: Monocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.
Published: 2022

10. Recherche translationnelle entre espèces modèles et cultivées :la génomique comparative pour la sélection végétale

Author: Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)
Subjects: Paleogenomics, Modèles, Cultures, Models, Evolution, [SDV]Life Sciences [q-bio], Paléogénomique, Improvement, Amélioration, Crops, Évolution, General Medicine, Adaptation
Abstract: International audience; The concept of translational research, which originated in the medical field in the 1980s,consists in improving the efficient transfer of research results obtained in a species (which can be considered as a model or pivot) to all the species for which these results are of interest for its improvementin Agriculture. In this context, comparative genomics is an important tool for translational research,effectively identifying genes controlling common functions between species. Editing and phenotypingtools must thus allow the functional validation of the gene conserved within the species for which theknowledge has been extrapolated, that is to say transferred, and the identification of the best allelesand associated genotypes for exploitation in current breeding programs; é. Le concept de recherche translationnelle, issu du domaine médical dans les années 80,consiste à améliorer le transfert efficace des résultats de recherche obtenus chez une espèce (pouvantêtre considéré comme modèle ou pivot) à l’ensemble des espèces pour lesquelles ces résultats sontd’intérêt pour son amélioration en agriculture. Dans ce contexte, la génomique comparée constitueun outil important de la recherche translationnelle en identifiant efficacement les gènes contrôlantdes fonctions communes entre espèces. Les outils d’édition génomique, de criblage de diversitégénétique et de phénotypage doivent ainsi permettre la validation fonctionnelle du gène conservé ausein de l’espèce chez laquelle la connaissance a été extrapolée à partir de l’espèce pivot, c’est-à-diretransférée, ainsi que l’identification des meilleurs allèles et génotypes associés pour leur exploitationdans les programmes actuels de sélection
Published: 2022

11. 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

12. A Chromosome-Level Genome Assembly of the European Beech (

Author: Bagdevi, Mishra, Bartosz, Ulaszewski, Joanna, Meger, Jean-Marc, Aury, Catherine, Bodénès, Isabelle, Lesur-Kupin, Markus, Pfenninger, Corinne, Da Silva, Deepak K, Gupta, Erwan, Guichoux, Katrin, Heer, Céline, Lalanne, Karine, Labadie, Lars, Opgenoorth, Sebastian, Ploch, Grégoire, Le Provost, Jérôme, Salse, Ivan, Scotti, Stefan, Wötzel, Christophe, Plomion, Jaroslaw, Burczyk, and Marco, Thines
Abstract: The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in
Published: 2021

13. 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

14. A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs

Author: Bagdevi Mishra, Bartosz Ulaszewski, Joanna Meger, Jean-Marc Aury, Catherine Bodénès, Isabelle Lesur-Kupin, Markus Pfenninger, Corinne Da Silva, Deepak K Gupta, Erwan Guichoux, Katrin Heer, Céline Lalanne, Karine Labadie, Lars Opgenoorth, Sebastian Ploch, Grégoire Le Provost, Jérôme Salse, Ivan Scotti, Stefan Wötzel, Christophe Plomion, Jaroslaw Burczyk, and Marco Thines
Subjects: Nuclear gene, Chromosome 4, Fagus sylvatica, biology, Evolutionary biology, Chromosome, Sequence assembly, Single-nucleotide polymorphism, biology.organism_classification, Genome, Beech
Abstract: The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Published: 2021

15. 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

16. 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

17. 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

18. Model-Driven Multidisciplinary Global Research to Meet Future Needs: The Case for 'Improving Radiation Use Efficiency to Increase Yield'

Author: Brian L. Beres, Pierre Martre, P. Stephen Baenziger, Hans-Joachim Braun, Jacques Le Gouis, Jérôme Salse, M. Fernanda Dreccer, Matthew P. Reynolds, Frank Ewert, Senthold Asseng, Peter Langridge, University of Florida [Gainesville] (UF), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), 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), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Agriculture and Agri-Food [Ottawa] (AAFC), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Adelaide, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of Nebraska System, and Agriculture and Agri-Food (AAFC)
Subjects: 2. Zero hunger, 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Yield (finance), 04 agricultural and veterinary sciences, Agricultural engineering, 15. Life on land, Biology, 01 natural sciences, Multidisciplinary approach, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Improving wheat (Triticum aestivum L.) yields to meet the projected demand for food in the future requires the talents of diverse scientists. In this article, we present the rationale for crop-model-driven, trait-focused collaborative research emphasizing radiation use efficiency (RUE). Improving RUE is one of the promising avenues to substantially increase potential yields. A collaboration of crop modelers, physiologists, geneticists, plant breeders, and system agronomists is proposed to efficiently create genetic improvements that, when taken to the field, will have regional and global yield impacts. The effort will require a large, internationally integrated science project and related infrastructure such as was recently developed in the Wheat Initiative. The Wheat Initiative is an international consortium of scientists and public and industry funders to sustainably improve global wheat production. The proposed integrated research is applicable to explore other traits and trait combinations and could become a model for yield improvements for major food crops.
Published: 2019

19. 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

20. 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

21. 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

22. 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

23. 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

24. An integrated information system dedicated to oak genomics and genetics

Author: Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, Corinne da Silva, Sébastien Duplessis, Francois Ehrenmann, Sébastien Faye, Christine Gaspin, Christophe Klopp, Karine Labadie, Isabelle Lesur, Thibault Leroy, Florent Murat, Olivier Rué, Catherine Bodenes, Jean-Charles Leplé, Grégoire Le Provost, Patricia Faivre Rampant, Antoine Kremer, Francis Martin, Hadi Quesneville, Jérôme Salse, Christophe Plomion, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), 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), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: Oak, [SDV]Life Sciences [q-bio], Genetics, Genomics, Information system
Abstract: GnpIS is an information system designed to integrate and link genomic, genetic and environmental data into a single environment dedicated to plant (crops and forest trees) and fungi data. GnpIS is regularly improved with new functionalities answering specific needs raised by scientists and released several times a year. We propose to illustrate the integrated genome annotation system we set up with a focus on the interoperability between genomic and genetic data (e.g. Markers, QTL) present in GnpIS-core, through the use case Quercus robur (the pedunculate oak), a large, complex and highly heterozygous genome.This genome annotation system relies on GMOD interfaces such as WebApollo/JBrowse and Intermine to make these data available under a user-friendly environment. All annotations and analysis results (Transposable Elements (TEs), genes, ncRNA ...) and functional annotation (protein-coding genes) were obtained using powerful and robust pipelines: (i) REPET used to detect, classify and annotate TEs representing 50% of the genome; (ii) Eugene which integrates ab initio and similarity gene finding softwares to predict gene models; (iii) ncRNA were annotated using different tools to annotate lncRNA, miRNA, rRNA, tRNA (iv) A functional annotation pipeline mainly based on Interproscan and comparative genomics was performed on the 25,808 highly confident predicted proteins. This system allows experts to analyze their protein families of interest and curate/validate gene structure.All together these resources provide a framework to study the two key evolutionary processes that explain the remarkable diversity found within the Quercus genus: local adaptation and speciation.
Published: 2018

25. Retour sur les 13èmes Rencontres d’Archéobotanique 2018 : La carpologie et l’interdisciplinarité : approches intégrées, tenues du 27 février au 2 mars 2018 à Besse et Saint‑Anastaise (Auvergne, France). Compte rendu du débat de prospective archéobotanique Favoriser l’émergence de nouvelles thématiques, développer l’interdisciplinarité, structurer la communauté. Quels moyens ? Quelles actions possibles ?

Author: Manon Cabanis, Caroline Schaal, Marie-France Dietsch, Christel Fraisse, Sébastien Gaime, Philippe Marinval, Henri-Georges Naton, Patrick Pion, Vanessa Py-Saragaglia, Jérôme Salse, and Christophe Tufféry
Subjects: Archéobotanique, Archéométrie, Paléoenvironnements, Carpologie, Ecofacts, France, Holocène
Abstract: Cabanis Manon,Schaal Caroline,Dietsch Marie-France,Fraisse Christel,Gaime Sébastien,Marinval Philippe,Naton Henri-Georges,Pion Patrick,Py-Saragaglia Vanessa,Salse Jérôme,Tufféry Christophe. Retour sur les 13èmes Rencontres d’Archéobotanique 2018 : La carpologie et l’interdisciplinarité : approches intégrées, tenues du 27 février au 2 mars 2018 à Besse et Saint‑Anastaise (Auvergne, France). Compte rendu du débat de prospective archéobotanique Favoriser l’émergence de nouvelles thématiques, développer l’interdisciplinarité, structurer la communauté. Quels moyens ? Quelles actions possibles ?. In: Le Journal de botanique, n°84, 2018. Décembre. pp. 13-16.
Published: 2018

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. ECHAP : un projet pour identifier les possibilités de réduction de l’utilisation des fongicides en utilisant l’architecture des couverts

Author: Corinne Robert, Christian Fournier, Mariem Abichou, Bruno Andrieu, Marie-Odile Bancal, Enrique Barriuso, Carole Bedos, Pierre Benoit, Valerie Bergheaud, Marc Bidon, Bernard Bonicelli, Camille Chambon, Chapuis, R., Eric Cotteux, Da Costa, J., Brigitte Durand, Nathalie Gagnaire, Damien Gaudillat, Christophe Gigot, Guillaume Girardin, David Gouache, Josiane Jean-Jacques, Laure Mamy, Bertrand Ney, Paveley, N., Benjamin Perriot, Samuel Poidevin, Stéphanie Pointet, Valerie Pot-Genty, Christophe Pradal, Richard, C., Sébastien Saint-Jean, Jérôme Salse, Carole Sinfort, Smith, J., Ter Halle, A., Den Berg, E., Anne-Sophie Walker, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), ARVALIS - Institut du végétal [Paris], Agricultural Development and Advisory Service, 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), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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)-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), ALTERRA, BIOlogie et GEstion des Risques en agriculture (BIOGER), Groupe Français des Pesticides (GFP). FRA., 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), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Blaise Pascal (Clermont Ferrand 2) (UBP), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Alterra Green World Research (ALTERRA), AgroParisTech-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), 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 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), 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)-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)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: architecture, ComputingMilieux_THECOMPUTINGPROFESSION, GeneralLiterature_INTRODUCTORYANDSURVEY, traitements, [SDV]Life Sciences [q-bio], septoriose, stomatognathic diseases, fongicides, architechure, InformationSystems_MODELSANDPRINCIPLES, blé, ComputingMilieux_COMPUTERSANDEDUCATION, ComputerSystemsOrganization_SPECIAL-PURPOSEANDAPPLICATION-BASEDSYSTEMS, modélisation
Abstract: ECHAP : un projet pour identifier les possibilités de réduction de l’utilisation des fongicides en utilisant l’architecture des couverts. 45e Congrès du Groupe Français des Pesticides Devenir et impact des pesticides : verrous à lever et nouveaux enjeux
Published: 2015

40. 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

41. 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

42. 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

43. Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

Author: Hadi Quesneville, Raphael Flores, Florent Murat, Delphine Steinbach, Sébastien Guizard, Rongzhi Zhang, Haris Gavranović, Eric Tannier, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), PCSV, Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), University of Sarajevo, UNIVERZITET U SARAJEVU, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), 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-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)-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), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), UNIVERSITY OF SARAJEVO - UNIVERZITET U SARAJEVU, 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 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-Université Lumière - Lyon 2 (UL2)-Inria Grenoble - Rhône-Alpes, 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-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), 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), and Université de Lyon-Université Lumière - Lyon 2 (UL2)
Subjects: Crops, Agricultural, Plasticity, Evolution, Bioinformatics, Karyotype, Lotus, dominance, paleogenomics, evolution, polyploidy, plasticity, Vitaceae, Synteny, Genome, Chromosomes, Plant, Polyploidy, Evolution, Molecular, Magnoliopsida, Gene Duplication, Gene Order, Botany, Genetics, Gene, Dominance, Phylogeny, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, biology, Brassicaceae, Genomics, Fabaceae, 15. Life on land, biology.organism_classification, Paleogenomics, Bio-informatique, Ploidy, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Plant, Research Article
Abstract: International audience; We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, “DicotSyntenyViewer” (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
Published: 2015

44. Brachypodium Paleogenomics: From Genome Evolution to Translational Research in Grass Crops

Author: Jérôme Salse
Subjects: Genome evolution, biology, Evolutionary biology, Gene duplication, food and beverages, Chromosome, Brachypodium, Brachypodium distachyon, biology.organism_classification, Genome, Gene, Synteny
Abstract: The modern Brachypodium distachyon genome consisting in 25,532 genes, 271 Megabases covering five chromosomes derives from a founder grass ancestor structured in 7/12 protochromosomes containing 10,000–15,000 protogenes with a minimal physical coding space size of
Published: 2015

45. FRIZZY PANICLE drives supernumerary spikelets in bread wheat

Author: N. Watanabe, Alexander A. Krasnikov, Yuriy L. Orlov, Florent Murat, Lyudmila Laikova, Audrey Chosson, Charles Poncet, Caroline Pont, Petr Martinek, Elena A. Salina, Nadine Gautier, Hélène Bergès, O. B. Dobrovolskaya, Richard Sibout, Ekaterina D. Badaeva, Véronique Gautier, Jérôme Salse, and Elisa Prat
Subjects: 2. Zero hunger, Genetics, biology, Physiology, Mutant, food and beverages, Plant Science, Flowers, Articles, biology.organism_classification, Genes, Plant, Phenotype, Frameshift mutation, Inflorescence, Genetic Loci, Botany, Supernumerary, Triticeae, Frameshift Mutation, Gene, Triticum, Panicle
Abstract: Bread wheat (Triticum aestivum) inflorescences, or spikes, are characteristically unbranched and normally bear one spikelet per rachis node. Wheat mutants on which supernumerary spikelets (SSs) develop are particularly useful resources for work towards understanding the genetic mechanisms underlying wheat inflorescence architecture and, ultimately, yield components. Here, we report the characterization of genetically unrelated mutants leading to the identification of the wheat FRIZZY PANICLE (FZP) gene, encoding a member of the APETALA2/Ethylene Response Factor transcription factor family, which drives the SS trait in bread wheat. Structural and functional characterization of the three wheat FZP homoeologous genes (WFZP) revealed that coding mutations of WFZP-D cause the SS phenotype, with the most severe effect when WFZP-D lesions are combined with a frameshift mutation in WFZP-A. We provide WFZP-based resources that may be useful for genetic manipulations with the aim of improving bread wheat yield by increasing grain number.
Published: 2014

46. Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat

Author: Jérôme Salse, Matthew P. Reynolds, Ravi Valluru, Int Maize & Wheat Improvement Ctr, CIMMYT, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Genomics, Biology, Quantitative trait locus, Breeding, Crop, Metabolomics, Genetics, Photosynthesis, Triticum, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Comparative Genomic Hybridization, Resistance (ecology), business.industry, food and beverages, Oryza, General Medicine, 15. Life on land, Phenotype, Adaptation, Physiological, Biotechnology, Agronomy, Agriculture, Adaptation, business, Agronomy and Crop Science
Abstract: International audience; Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.
Published: 2014

47. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Author: William G. Farmerie, Chunxian Chen, Marcos A. Machado, Daniel Ramón, Jarrod Chapman, Patrick Wincker, Dominique Brunel, Jerry Jenkins, Juan V. Munoz-Sanz, Mohammed Mohiuddin, Javier Terol, Victoria Ibanez, Simone Scalabrin, Giuseppe Reforgiato, Amparo Herrero-Ortega, Cristian Del Fabbro, Xavier Perrier, Jeremy Schmutz, Simon E. Prochnik, Jérôme Salse, Kamel Jabbari, Uffe Hellsten, Julie Poulain, Daniel S. Rokhsar, Alexandre Lomsadze, Karin M. Fredrikson, Andrea Zuccolo, Francisco R. Tadeo, Leandro H. Estornell, Luis Navarro, Olivier Jaillon, Brian Desany, Frederick G. Gmitter, François Luro, Federica Cattonaro, G Albert Wu, Paul Burns, Francis Quetier, Marco Aurélio Takita, Mark Borodovsky, Manuel Talon, Tim Harkins, Julián Pérez-Pérez, Jane Grimwood, Pablo Aleza, Florent Murat, Mikeal L. Roose, Patrick Ollitrault, Michele Morgante, Karine Labadie, Arnaud Couloux, Sara Pinosio, Juliana Freitas-Astúa, Manuel Ruiz, Chinnappa D. Kodira, United States Department of Energy, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), DOE Joint Genome Institute [Walnut Creek], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Applied Genomics Institute (IGA), Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research (IVIA), 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), 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), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, Plant Genetics Institute, Consiglio Nazionale delle Ricerche [Roma] (CNR), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centro de Genómica - Centre de Genòmica [IVIA], Department of Food Biotechnology, Biopolis, Universitat de València (UV), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Génétique et Ecophysiologie de la qualité des agrumes (GEQA), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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, Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine - University of Udine [Italie], National Science and Technology Institute of Genomics for Citrus Breeding, Brazil [FAPESP 08/57909-2, CNPq 573848/08-4], Brazilian Agricultural Research Corporation (Embrapa), Embrapa-Monsanto Agreement, Agence Nationale de la Recherche (ANR) [CITRUSSEQ PCS-08-GENO], program ANR Blanc-PAGE [ANR-2011-BSV6-00801], US National Institutes of Health [HG00783], Generalitat Valenciana, Spain [PrometeoII/2013/008], Ministry of Economy and Innovation-Fondo Europeo de Desarrollo Regional (FEDER), Spain [AGL2011-26490], Conselleria de Agricultura, Pesca, Alimentacion y Agua from the Generalitat Valenciana, Ministerio de Economia e Innovacion [PSE-060000-2009-8, IPT-010000-2010-43], Citruseq-Citrusgenn consortium company (Anecoop S. Coop., Eurosemillas S.A.), Citruseq-Citrusgenn consortium company (Fundacion Ruralcaja Valencia), Citruseq-Citrusgenn consortium company (GCM Variedades Vegetales A.I.E.), Citruseq-Citrusgenn consortium company ( Investigacion Citricola Castellon S.A.), Citruseq-Citrusgenn consortium company (Source Citrus Genesis-Special New Fruit Licensing, Ltd.), Florida Citrus Production Research Advisory Council (FCPRAC), Florida Department of Agriculture and Consumer Services [013646], Florida Department of Citrus (FDOC), Citrus Research and Development Foundation [71], Ministero delle Politiche Agricole Alimentari e Forestali, Project Citrustart, Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR), Programma Operativo Nazionale 'Ricerca e Competitivita', Project IT-Citrus Genomics [PON_01623], Office of Science of the US Department of Energy [DE-AC02-05CH11231], Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), 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), Instituto Valenciano de Investigaciones Agrarias, 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), Centro de Genomica, Valencian Institute of Agrarian Research (IVIA), 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), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), and 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)
Subjects: Germplasm, Phylogénie, Citrus, [SDV]Life Sciences [q-bio], Plant genetics, Orange (colour), Breeding, Applied Microbiology and Biotechnology, F30 - Génétique et amélioration des plantes, Domestication, Citrus clementina, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Genome, food and beverages, F70 - Taxonomie végétale et phytogéographie, séquençage du génome, Molecular Medicine, Ploidy, Sequence Analysis, Citrus × sinensis, Genome, Plant, Biotechnology, Citrus sinensis, Crops, Agricultural, Séquence nucléotidique, Evolution, Molecular Sequence Data, Biomedical Engineering, Bioengineering, Agrume, Crops, Biology, Article, Evolution, Molecular, Citrus maxima, Species Specificity, Phylogenetics, Botany, Hybrid, Génie génétique, Agricultural, Génome, Base Sequence, Molecular, Genetic Variation, Taxonomie, Sequence Analysis, DNA, DNA, Plant, next-generation sequencing, Citrus reticulata
Abstract: Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes- and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement., 栽培されている柑橘類は、野生祖先種から選択されたもの、またはその交雑種であるが、その祖先種の正体、および柑橘類栽培化に対する寄与には依然として議論がある。今回、柑橘類ゲノム（クレメンタインの高精度標準ハプロイドゲノム、ならびにマンダリン、パメロ、スイートオレンジ、およびサワーオレンジのゲノム）の配列解読および比較を行ったところ、栽培種が2つの祖先種に由来することが明らかにされた。栽培パメロは単一祖先種 Citrus maxima から選択されたことがわかったが、栽培マンダリンは祖先マンダリン種 Citrus reticulata に C. maxima から遺伝子移入が行われたものであった。最も広く栽培されている柑橘類であるスイートオレンジは過去に混種した個体の子孫であるが、サワーオレンジは純粋な C. maxima と C. reticulata とのF1雑種であり、このことは、野生のマンダリンが初期の育種生殖系列の要素であったことを意味している。中国の野生「マンダリン」は C. reticulata とは大きく異なっており、別の未確認の野生柑橘種である可能性が示唆される。ゲノム解析で柑橘類の系統発生を理解することにより、分類学的な関係が解明され、配列本位の遺伝的改良が促進される。
Published: 2014

48. The genome of Eucalyptus grandis

Author: Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), 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, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)
Subjects: Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract: International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
Published: 2014

49. Paleo-evolutionary plasticity of plant disease resistance genes

Author: Jérôme Salse, Caroline Pont, Thierry Langin, Rongzhi Zhang, Florent Murat, Génétique Diversité et Ecophysiologie des Céréales (GDEC), 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), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Agence Nationale de la Recherche (program ANR Blanc-PAGE) [ANR-2011-BSV6-00801]
Subjects: Plasticity, Duplication, Evolution, [SDV]Life Sciences [q-bio], Biology, Plant disease resistance, Genome, Evolution, Molecular, Polyploidy, duplication de gènes, Gene Duplication, Gene duplication, Genetics, Copy-number variation, R-genes, évolution, Eudicots, Gene, ComputingMilieux_MISCELLANEOUS, Disease Resistance, Plant Diseases, Plant Proteins, Plant evolution, plasticité, food and beverages, Plants, gène de résistance, maladie des plantes, MicroRNAs, Evolutionary biology, DNA microarray, Genome, Plant, Research Article, Biotechnology
Abstract: International audience; Background: The recent access to a large set of genome sequences, combined with a robust evolutionary scenario of modern monocot (i.e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the opportunity to gain insights into disease resistance genes (R-genes) evolutionary plasticity. Results: We unravel in the current article (i) a R-genes repertoire consisting in 7883 for monocots and 15758 for eudicots, (ii) a contrasted R-genes conservation with 23.8% for monocots and 6.6% for dicots, (iii) a minimal ancestral founder pool of 384 R-genes for the monocots and 150 R-genes for the eudicots, (iv) a general pattern of organization in clusters accounting for more than 60% of mapped R-genes, (v) a biased deletion of ancestral duplicated R-genes between paralogous blocks possibly compensated by clusterization, (vi) a bias in R-genes clusterization where Leucine-Rich Repeats act as a 'glue' for domain association, (vii) a R-genes/miRNAs interome enriched toward duplicated R-genes. Conclusions: Together, our data may suggest that R-genes family plasticity operated during plant evolution (i) at the structural level through massive duplicates loss counterbalanced by massive clusterization following polyploidization; as well as at (ii) the regulation level through microRNA/R-gene interactions acting as a possible source of functional diploidization of structurally retained R-genes duplicates. Such evolutionary shuffling events leaded to CNVs (i.e. Copy Number Variation) and PAVs (i.e. Presence Absence Variation) between related species operating in the decay of R-genes colinearity between plant species.
Published: 2014

50. Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

Author: Florent Murat, Jérôme Salse, Alix Armero, Delphine Steinbach, Caroline Pont, Raphael Flores, Sébastien Guizard, Rongzhi Zhang, Richard Cooke, Hadi Quesneville, 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), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), 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), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)
Subjects: Duplication, [SDV]Life Sciences [q-bio], syntenie, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Genome, Gene Duplication, Gene duplication, évolution, Phylogeny, ComputingMilieux_MISCELLANEOUS, Genes, Dominant, Recombination, Genetic, Genetics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], synteny, food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Karyotype, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], duplication, Recombination, Research Article, Evolution, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Genes, Plant, Poaceae, dominance, Synteny, Chromosomes, Plant, Evolution, Molecular, Polyploidy, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], genome, Ecology, Evolution, Behavior and Systematics, Dominance, Comparative genomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, génome, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, ancestor, Ancestor, Gene Deletion, Software
Abstract: International audience; Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
Published: 2013

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