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1. Plant-PLMview: a database for identifyingcis-regulatory sequences with preferential positions in gene-proximal regions of plants

Author

Julien Rozière, Franck Samson, Cécile Guichard, Margot Correa, Sylvie Coursol, Marie-Laure Martin, and Véronique Brunaud

Abstract

BackgroundEstablishing relationships between transcription factors and target genes is essential for understanding the mechanisms regulating gene expression, which play a fundamental role in plant adaptation to the local environment. Despite the importance of this research area and the tremendous progress in sequencing methods such as ChIP-seq and DAP-seq, we are still far from a complete reconstruction of thecis-regulatory landscape. Only a small number of transcription factors can be assessed from experimental data to identify theircis-regulatory binding sites. This highlights the role thatin silicoapproaches can play to complement experimental data.ResultsWe have developed Plant-PLMview, a web-accessible database for detecting preferentiallycis-regulatory sequences in the gene-proximal regions of 20 plant species. Users of Plant-PLMview can (i) access the proximal regions of controlled genes from 20 plant species, (ii) query their own DNA motifs or access 840cis-regulatory sequences from various plant resources, and (iii) use a tool called PLMdetect to search for preferentially located motifs in the gene-proximal regions of a list of genes. Results are displayed via a web interface with a list of DNA motifs preferentially located in a region near the start or end of genes, the distribution of these motifs and associated annotations. In addition, a graphical map of the preferential locations of the motifs in the 5’ and 3’-proximal regions of genes provides an overview of all motifs and genes examined.ConclusionPlant-PLMview provides the opportunity to study the proximal landscape of gene regulation in 20 plant genomes. The originality of the database lies in its ease of use thanks to the curated data (cis-regulatory sequences and proximal regions of genes) and the possibility to search through PLMdetect in the 5’-gene-proximal region, but also in the 3’-gene-proximal region, which is rarely explored. The web interface provides numerous graphical views that allow the users to get an overview and interpret the results more easily.

Published
2022
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3. The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

Author

Bérengère Bouillon, Emmanuelle Lerat, Franck Samson, Kévin Normand, Margot Correa, Carène Rizzon, Etienne Birmelé, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Mathématiques Appliquées Paris 5 (MAP5 - UMR 8145), Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Recherche Mathématique Avancée (IRMA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-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), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
Transposable element, AcademicSubjects/SCI01140, LINE, Retrotransposon, Biology, Genome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Gene Duplication, Gene duplication, Genetics, essential genes, Animals, Humans, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Short Interspersed Nucleotide Elements, Regulation of gene expression, Mammals, Recombination, Genetic, 0303 health sciences, Base Composition, Genes, Essential, Genome, Human, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], AcademicSubjects/SCI01130, food and beverages, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], SINE, chemistry, Evolutionary biology, gene evolution, DNA Transposable Elements, Human genome, transposable elements, Erratum, 030217 neurology & neurosurgery, DNA, Research Article
Abstract

Erratum: https://doi.org/10.1093/gbe/evab175; International audience; Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes.

Published
2021
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5. Genetic diversity of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile

Author

Géraldine Groussier, Tania Zaviezo, Paul Amouroux, P. Kreiter, J. F. Germain, Thibaut Malausa, Margot Correa, J. Ampuero, Didier Crochard, Facultad de Agronomía e Ingeniería Forestal [Chile], Pontificia Universidad Católica de Chile (UC), Departamento de Fruticultura y Enologia, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Laboratoire de santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-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), Xilema (ANASAC Control Biol), This project was supported by the EU FP7 Marie Curie IAPP Project 'Colbics' #324475 and by the 'Fundación para la Innovación Agraria' (FIA) #PYT-2015-0230., European Project: 324475,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IAPP,COLBICS(2013), Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Catolica de Chile, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Fac Agron & Ingn Forestal, Dept Fruticultura & Enol, 'Fundacion para la Innovacion Agraria' (FIA) PYT-2015-0230, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
0106 biological sciences, haplotype, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Science, hemiptera, Population, Zoology, sternorrhyncha, Diaspididae, 010603 evolutionary biology, 01 natural sciences, Article, Electron Transport Complex IV, scale, diaspididae, Botany, Animals, education, Phylogeny, Coccidae, Aspidiotus nerii, Genetic diversity, education.field_of_study, Multidisciplinary, biology, coccoidea, Genetic Variation, biology.organism_classification, écaille, Hemiptera, Sternorrhyncha, genêtic variation, 010602 entomology, scale insects, Genes, Mitochondrial, Haplotypes, diversité génétique, Medicine, aspidiotus nerii, Coccus hesperidum
Abstract

Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees. We sequenced the COI and 28S genes in each population. In total, 19 Diaspididae species and 11 Coccidae species were identified morphologically. From the 63 COI haplotypes and the 54 28S haplotypes uncovered, and using several DNA data analysis methods (Automatic Barcode Gap Discovery, K2P distance, NJ trees), up to 36 genetic clusters were detected. Morphological and DNA data were congruent, except for three species (Aspidiotus nerii, Hemiberlesia rapax and Coccus hesperidum) in which DNA data revealed highly differentiated lineages. More than 50% of the haplotypes obtained had no high-scoring matches with any of the sequences in the GenBank database. This study provides 63 COI and 54 28S barcode sequences for the identification of Coccoidea from Chile.

Published
2017
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6. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Author

Gaëtan Droc, Adriana Alberti, Philippe Francois, Rémy Habas, Patrick Wincker, Jaroslav Dolezel, Mouna Jeridi, Cyril Jourda, E. Hribova, Thomas Wicker, Kamel Jabbari, Julie Leclercq, Cees Waalwijk, Olivier Panaud, Benjamin Noel, Marlã̈ne Souquet, Manuel Ruiz, Didier Mbéguié-A-Mbéguié, Margot Correa, Nicolas Roux, Saravanaraj Ayyampalayam, Ronan Rivallan, Spencer Brown, Françoise Carreel, Maria Bernard, Andrzej Kilian, Jose Barbosa, Olivier Jaillon, Olivier Garsmeur, Jean-Marc Aury, Ange-Marie Risterucci, Julie Poulain, Karine Labadie, Xavier Argout, Steeve Joseph, Pat Heslop-Harrison, Jean-Christophe Glaszmann, Ana Maria Rocha de Almeida, Mathieu Rouard, Jean Weissenbach, Stéphanie Bocs, Juliette Lengellé, Nabila Yahiaoui, Eric Lyons, Anne Dievart, Corinne Da Silva, Marguerite Rodier-Goud, Dheema Burthia, Céline Cardi, Michael Freeling, Angélique D'Hont, Claire Poiron, Valentin Guignon, Matthieu Chabannes, Frédéric Bakry, Christophe Jenny, Franc-Christophe Baurens, Michael R. McKain, Miguel A. Dita, Francis Quetier, Diane Burgess, Jim Leebens-Mack, Gert H. J. Kema, 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), 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), 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Optique Atmosphérique - UMR 8518 (LOA), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), 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), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Wageningen University and Research Centre [Wageningen] (WUR), University of Zurich, and D'Hont, Angélique

Subjects
MESH: Genome, Plant, 0106 biological sciences, Phylogénie, Lineage (evolution), Plant genetics, Évolution, 580 Plants (Botany), Haploidy, resource, in-situ hybridization, Musa acuminata, 01 natural sciences, F30 - Génétique et amélioration des plantes, MESH: Genotype, sequence count data, 10126 Department of Plant and Microbial Biology, Gene Duplication, Musa balbisiana, dna sequences, MESH: Genes, Plant, maximum likelihood, MESH: Phylogeny, Conserved Sequence, Phylogeny, MESH: Evolution, Molecular, 2. Zero hunger, 0303 health sciences, MESH: Conserved Sequence, Multidisciplinary, MESH: Gene Duplication, food and beverages, F70 - Taxonomie végétale et phytogéographie, MESH: Haploidy, MESH: DNA Transposable Elements, Génotype, Genome, Plant, dna-sequences, Séquence nucléotidique, diversification, Poales, Genotype, Molecular Sequence Data, Biology, Poaceae, Genes, Plant, differential expression, Evolution, Molecular, Zingiberales, Biointeractions and Plant Health, 03 medical and health sciences, MESH: Musa, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gene, Domestication, 030304 developmental biology, 1000 Multidisciplinary, Génome, MESH: Molecular Sequence Data, Bioint Moleculair Phytopathology, rice, Musa, 15. Life on land, biology.organism_classification, Arecales, DNA Transposable Elements, identification, maximum-likelihood, in situ hybridization, 010606 plant biology & botany
Abstract

International audience; Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.

Published
2012
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7. Erratum for the Report: 'Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome' by B. Chalhoub, F. Denoeud, S. Liu, I. A. P. Parkin, H. Tang, X. Wang, J. Chiquet, H. Belcram, C. Tong, B. Samans, M. Corréa, C. Da Silva, J. Just, C. Falentin, C. S. Koh, I. Le Clainche, M. Bernard, P. Bento, B. Noel, K. Labadie, A. Alberti, M. Charles, D. Arnaud, H. Guo, C. Daviaud, S. Alamery, K. Jabbari, M. Zhao, P. P. Edger, H. Chelaifa, D. Tack, G. Lassalle, I. Mestiri, N. Schnel, M.-C. Le Paslier, G. Fan, V. Renault, P. E. Bayer, A. A. Golicz, S. Manoli, T.-H. Lee, V. Ha Dinh Thi, S. Chalabi, Q. Hu, C. Fan, R. Tollenaere, Y. Lu, C. Battail, J. Shen, C. H. D. Sidebottom, X. Wang, A. Canaguier, A. Chauveau, A. Bérard, G. Deniot, M. Guan, Z. Liu, F. Sun, Y. P. Lim, E. Lyons, C. D. Town, I. Bancroft, X. Wang, J. Meng, J. Ma, J. C. Pires, G. J. King, D. Brunel, R. Delourme, M. Renard, J.-M. Aury, K. L. Adams, J. Batley, R. J. Snowdon, J. Tost, D. Edwards, Y. Zhou, W. Hua, A. G. Sharpe, A. H. Paterson, C. Guan, P. Wincker

Author

Aurélie Canaguier, Christophe Battail, Jean-Marc Aury, Christopher D. Town, Christian Daviaud, David C. Tack, Wei Hua, Christine Sidebottom, Shengyi Liu, Reece Tollenaere, Sahana Manoli, Graham J.W. King, Fengming Sun, J. Shen, Victor Renault, Philipp E. Bayer, I. Le Clainche, Jacqueline Batley, Ian Bancroft, Nicolas Schnel, M. C. Le Paslier, Dominique Arnaud, Karine Labadie, Agnieszka A. Golicz, Dominique Brunel, Smahane Chalabi, Hui Guo, Yongming Zhou, Eric Lyons, Pascal Bento, Gilles Lassalle, Chunyun Guan, Yong Pyo Lim, Imen Mestiri, J. C. Pires, Guangyi Fan, Houda Chelaifa, Mei Guan, Tae-Ho Lee, Harry Belcram, Qiong Hu, F. Denoeud, Aurélie Chauveau, Andrew G. Sharpe, Bernard Noël, Boulos Chalhoub, Chaobo Tong, Adriana Alberti, Patrick Wincker, Jinling Meng, Birgit Samans, Patrick P. Edger, C. Da Silva, Margot Correa, Jianxin Ma, Régine Delourme, Keith L. Adams, Meixia Zhao, Haibao Tang, David Edwards, Andrew H. Paterson, Cyril Falentin, Zhongsong Liu, Julien Chiquet, Y. Lu, Xinfa Wang, Jérémy Just, V. Ha Dinh Thi, Kamel Jabbari, Chuchuan Fan, G. Deniot, Rod J. Snowdon, Jörg Tost, Aurélie Bérard, Mathieu Charles, Michel Renard, Salman Alamery, Maria Bernard, Isobel A. P. Parkin, and Chu Shin Koh

Subjects
Multidisciplinary, Botany, Brassica, Biology, biology.organism_classification, Genome
Published
2014
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8. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author

Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, 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), 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), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-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), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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 California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, 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 ), 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 ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract

Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782

Published
2014
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9. A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants

Author

Margot Correa, Didier Auboeuf, Martin Dutertre, and Pierre de la Grange

Subjects
Proteome, Polyadenylation, Information Storage and Retrieval, Biology, lcsh:Computer applications to medicine. Medical informatics, computer.software_genre, Biochemistry, Database, Mice, Exon, Structural Biology, Databases, Genetic, Gene expression, Animals, Humans, lcsh:QH301-705.5, Gene, Molecular Biology, Genetics, Applied Mathematics, Alternative splicing, Chromosome Mapping, Genetic Variation, Computer Science Applications, lcsh:Biology (General), Gene Expression Regulation, RNA splicing, lcsh:R858-859.7, Database Management Systems, Human genome, RNA Splice Sites, DNA microarray, computer, Transcription Factors
Abstract

Background Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the diversity of the transcriptome, there is a need for interactive databases that provide information about the potential function of each splicing variant, as well as its expression pattern. Description After setting up a database in which human and mouse splicing variants were compiled, we developed tools (1) to predict the production of protein isoforms from these transcripts, taking account of the presence of open reading frames and mechanisms that could potentially eliminate transcripts and/or inhibit their translation, i.e. nonsense-mediated mRNA decay and microRNAs; (2) to support studies of the regulation of transcript expression at multiple levels, including transcription and splicing, particularly in terms of tissue specificity; and (3) to assist in experimental analysis of the expression of splicing variants. Importantly, analyses of all features from transcript metabolism to functional protein domains were integrated in a highly interactive, user-friendly web interface that allows the functional and regulatory features of gene transcripts to be assessed rapidly and accurately. Conclusion In addition to identifying the transcripts produced by human and mouse genes, fast DB http://www.fast-db.com provides tools for analyzing the putative functions of these transcripts and the regulation of their expression. Therefore, fast DB has achieved an advance in alternative splicing databases by providing resources for the functional interpretation of splicing variants for the human and mouse genomes. Because gene expression studies are increasingly employed in clinical analyses, our web interface has been designed to be as user-friendly as possible and to be readily searchable and intelligible at a glance by the whole biomedical community.

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