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1. Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion

Author

Alberto Cenci, Nathalie Chantret, and Mathieu Rouard

Subjects
glycosyltransferase family 61, Liliopsida, gene family expansion, positive selection footprints, orthologous genes, phylogeny, Plant culture, SB1-1110
Abstract

Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study.

Published
2018
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3. Domestication reduces alternative splicing expression variations in sorghum.

Author

Vincent Ranwez, Audrey Serra, David Pot, and Nathalie Chantret

Subjects
Medicine, Science
Abstract

Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.

Published
2017
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4. A New ‘Comprehensive’ Annotation of Leucine-Rich Repeat-Containing Receptors in Rice

Author

Christophe Périn, Céline Gottin, Vincent Ranwez, Gaëtan Droc, Anne Dievart, Marilyne Summo, Nathalie Chantret, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), CGIAR, Institut Agro, and CIRAD

Subjects
Repetitive Sequences, Amino Acid, Genotype, Population, pseudogenes, chemical and pharmacologic phenomena, Oryza sativa, LRR-receptor-like kinase, Computational biology, Plant disease resistance, Leucine-rich repeat, Biology, nucleotide-binding LRR receptor, Genome, F30 - Génétique et amélioration des plantes, Annotation, Leucine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Natural variability, education, Gene, H20 - Maladies des plantes, Plant Proteins, education.field_of_study, phytogénétique, fungi, food and beverages, annotation curation, Molecular Sequence Annotation, Oryza, LRR-receptor-like protein, Résistance aux maladies, disease resistance gene, Genome, Plant, Reference genome
Abstract

International audience; Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using LRRPROFILER, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties.

Published
2021
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5. Aligning Protein-Coding Nucleotide Sequences with MACSE

Author

Frédéric Delsuc, Nathalie Chantret, Vincent Ranwez, 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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 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), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), European Project: 65P3690(1965), 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 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0106 biological sciences, 0301 basic medicine, Nonsynonymous substitution, Computer science, Pseudogene, [SDV]Life Sciences [q-bio], Computational biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Molecular evolution, Phylogenomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nucleotide, Gene, Sequence (medicine), Protein coding, chemistry.chemical_classification, Multiple sequence alignment, Bioinformatics pipelines, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Stop codon, 030104 developmental biology, chemistry, Metabarcoding, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Pseudogenes
Abstract

International audience; Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/.

Published
2021
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6. Aligning Protein-Coding Nucleotide Sequences with MACSE

Author

Vincent, Ranwez, Nathalie, Chantret, and Frédéric, Delsuc

Subjects
Evolution, Molecular, Base Sequence, Animals, Computational Biology, Amino Acid Sequence, Genomics, Sequence Analysis, DNA, Sequence Alignment, Algorithms, Phylogeny, Pseudogenes, Software
Abstract

Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/ .

Published
2020

7. Origin and Diversity of Plant Receptor-Like Kinases

Author

Christophe Perin, Anne Dievart, Nathalie Chantret, Vincent Ranwez, Céline Gottin, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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 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), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, 0301 basic medicine, Phylogénie, Physiology, kinase, F60 - Physiologie et biochimie végétale, media_common.quotation_subject, receptor, [SDV]Life Sciences [q-bio], domain, Évolution, plant, Plant Science, Biology, Protein Serine-Threonine Kinases, 01 natural sciences, F30 - Génétique et amélioration des plantes, diversity, 03 medical and health sciences, Récepteurs, Variation génétique, origin, Gene family, RKRLK, Evolutionary dynamics, Molecular Biology, Phylogeny, media_common, Plant Proteins, Whole genome sequencing, Kinase, Cell Biology, Plants, Biological Evolution, 030104 developmental biology, Evolutionary biology, Genome, Plant, genetic processes [EN], 010606 plant biology & botany, Diversity (politics)
Abstract

International audience; Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results. © 2020 by Annual Reviews.

Published
2020
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8. Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion

Author

Nathalie Chantret, Alberto Cenci, Mathieu Rouard, CGIAR, 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), CGIAR Research Program on Roots, Tubers and Bananas (RTB), and Belgian Development Cooperation (DGD)

Subjects
0106 biological sciences, 0301 basic medicine, Genome evolution, gene family expansion, [SDV]Life Sciences [q-bio], Liliopsida, Plant Science, Biology, lcsh:Plant culture, phylogeny, 01 natural sciences, Genome, positive selection footprints, glycosyltransferase family 61, orthologous genes, 03 medical and health sciences, Phylogenetics, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Taxonomic rank, Clade, Gene, Segmental duplication, Original Research, fungi, food and beverages, 030104 developmental biology, Evolutionary biology, 010606 plant biology & botany
Abstract

International audience; Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study.

Published
2018
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9. MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Author

Nathalie Chantret, Cédric Cambon, Emmanuel J. P. Douzery, Vincent Ranwez, Frédéric Delsuc, 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), 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), Agence Nationale de la Recherche 'Investissements d'avenir/Bioinformatique' : ANR-10-BINF-01-02, Labex CeMEB 'Centre Mediterraneen de l'Environnement et de la Biodiversite' : ANR-10-LABX-0004, 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), 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), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0301 basic medicine, Nonsynonymous substitution, Pseudogene, [SDV]Life Sciences [q-bio], pseudogenes, Sequence alignment, Computational biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, Molecular evolution, Phylogenomics, Genetics, multiple sequence alignment, molecular evolution, phylogenomics, metabarcoding, Frameshift Mutation, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Multiple sequence alignment, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Resources, Stop codon, Agricultural sciences, 030104 developmental biology, Codon, Terminator, Sequence Alignment, Software, Sciences agricoles, Coding (social sciences)
Abstract

International audience; Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.

Published
2018
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10. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

Author

Gautier Sarah, Felix Homa, Stéphanie Pointet, Sandy Contreras, François Sabot, Benoit Nabholz, Sylvain Santoni, Laure Sauné, Morgane Ardisson, Nathalie Chantret, Christopher Sauvage, James Tregear, Cyril Jourda, David Pot, Yves Vigouroux, Hana Chair, Nora Scarcelli, Claire Billot, Nabila Yahiaoui, Roberto Bacilieri, Bouchaib Khadari, Michel Boccara, Adéline Barnaud, Jean-Pierre Péros, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin, Manuel Ruiz, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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 de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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)-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), Génétique et Amélioration des Fruits et Légumes (GAFL), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), This study was conducted in the framework of ARCAD (http://www.arcad-project.org), a project funded by Agropolis Fondation under the reference ID ARCAD 0900-001. GS, FH and SP salaries were supported by ARCAD budget. SC was supported by INRA (Division of Plant Biology and Breeding)., 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 de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), École pratique des hautes études (EPHE), and 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

Subjects
0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Reference transcriptomes, Évolution, comparative genomics, Genome, F30 - Génétique et amélioration des plantes, Population genomics, Plante sauvage, Contig Mapping, Génétique des populations, RNA-Seq, Pennisetum glaucum, 2. Zero hunger, Dioscorea, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Domestication des plantes, food and beverages, F70 - Taxonomie végétale et phytogéographie, Biological Evolution, ARN, Comparative genomics, essai comparatif, Genome, Plant, Biotechnology, Crops, Agricultural, Séquence nucléotidique, Biology, génomique, Crop, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Botany, Genetics, reference transcriptomes, Domestication, Blast2GO, Ecology, Evolution, Behavior and Systematics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Transcription génique, fungi, Digitaria exilis, 030104 developmental biology, Evolutionary biology, évolution génétique des populations, Metagenomics, Plante de culture, Transcriptome, Reference genome
Abstract

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.

Published
2017
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11. Corrigendum: New insights on leucine-rich repeats receptor-like kinase orthologous relationships in angiosperms

Author

Emmanuel Guiderdoni, Jean-François Dufayard, Christophe Périn, Nathalie Chantret, Gaëtan Droc, Mathilde Bettembourg, Iris Fischer, Anne Dievart, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0301 basic medicine, orthologs, angiosperme, kinase, receptor, LRR, Plant Science, lcsh:Plant culture, Biology, Leucine-rich repeat, phylogeny, 03 medical and health sciences, Phylogenetics, réponse au stress, phylogénie, lcsh:SB1-1110, Receptor, Receptor like kinase, Genetics, amélioration génétique, sélection génétique, Kinase, fungi, Microbiology and Parasitology, food and beverages, 04 agricultural and veterinary sciences, Microbiologie et Parasitologie, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, séquence riche en leucine, angiosperms
Abstract

AGAP : équipe ID / GE2pop; Corrigendum: New insights on leucine-rich repeats receptor-like kinase orthologous relationships in angiosperms

Published
2017
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12. Adaptation to climate through flowering phenology: a case study in Medicago truncatula

Author

Maxime Bonhomme, Jean Marie Prosperi, Nevin D. Young, Peter Tiffin, Nathalie Chantret, Concetta Burgarella, Joëlle Ronfort, Institut de Recherche pour le Développement (IRD), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Plant Biology, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Department of plant pathology, INRA (French National Institute of Agronomical Research) Department of Genetics and Plant Breeding, ARCAD, a flagship project of the Agropolis Foundation, NSF : 1237993, French laboratory of excellence project (LABEX) 'TULIP' : ANR-10-LABX-41, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Burgarella, Concetta, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, association genetics, Acclimatization, Climate, mixed model, Quantitative Trait Loci, climate adaptation, Flowers, flowering time, candidate genes, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, adaptation au climat, 03 medical and health sciences, Africa, Northern, Genetic variation, Genetics, Ecology, Evolution, Behavior and Systematics, Models, Genetic, floraison, Ecology, Phenology, fungi, food and beverages, medicago truncatula, 15. Life on land, biology.organism_classification, Phenotype, phénologie, Medicago truncatula, Agricultural sciences, Europe, Genetics, Population, 030104 developmental biology, 13. Climate action, Multigene Family, Trait, Adaptation, Sciences agricoles
Abstract

AGAP : équipe GEpop; International audience; Local climatic conditions likely constitute an important selective pressure on genes underlying important fitness-related traits such as flowering time and in many species flowering phenology and climatic gradients strongly covary. To test whether climate shapes genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large M. truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both climate variables and flowering phenotypes. Unlike genome-wide studies, candidate gene approaches are expected to enrich for the number of meaningful trait associations because they specifically target genes that are known to affect the trait of interest. We found that flowering time mediates adaptation to climatic conditions mainly by variation at genes located upstream in the flowering pathways, close to the environmental stimuli. Variables related to the annual precipitation regime reflected selective constraints on flowering time genes better than the other variables tested (temperature, altitude, latitude or longitude). By comparing phenotype and climate associations, we identified 12 flowering genes as the most promising candidates responsible for phenological adaptation to climate. Four of these genes were located in the known flowering time QTL region on chromosome 7. However, climate and flowering associations also highlighted largely distinct gene sets, suggesting different genetic architectures for adaptation to climate and flowering onset.

Published
2016
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13. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

Author

Iris Fischer, Jean-François Dufayard, Gaëtan Droc, Nathalie Chantret, Anne Dievart, 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), German Research Foundation : FI 1984/1-1, Agropolis Resource Center for Crop Conservation, Adaptation, and Diversity project of the Agropolis Foundation, Agence Nationale de la Recherche : ANR-08-GENM-021, and ANR-08-GENM-0021,RICE RLKO,Le phénome des LRR-RLK du riz : leur implication dans la réponse aux stress et les processus de développement par analyse systématique de K.O.s(2008)

Subjects
0301 basic medicine, Repetitive Sequences, Amino Acid, Subfamily, Time Factors, Physiology, F60 - Physiologie et biochimie végétale, [SDV]Life Sciences [q-bio], Amino Acid Motifs, Plant Science, Biology, Genome, F30 - Génétique et amélioration des plantes, Evolution, Molecular, 03 medical and health sciences, Magnoliopsida, Species Specificity, Phylogenetics, Gene Duplication, Gene duplication, Genetics, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Gene, Phylogeny, Plant Proteins, Plant evolution, Phylogenetic tree, Models, Genetic, fungi, Genetic Variation, Receptor Protein-Tyrosine Kinases, F70 - Taxonomie végétale et phytogéographie, Articles, 030104 developmental biology, Multigene Family
Abstract

AGAP : équipe GE2pop; International audience; Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a d(N)/d(S)-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.

Published
2016
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14. Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome

Author

Nathalie Chantret, Paulo Arruda, Nazeema Jannoo, Olivier Garsmeur, Angélique D'Hont, Laurent Grivet, and Jean-Christophe Glaszmann

Subjects
0106 biological sciences, 2. Zero hunger, Genetics, 0303 health sciences, biology, Saccharum spontaneum, food and beverages, Cell Biology, Plant Science, 15. Life on land, biology.organism_classification, 01 natural sciences, 7. Clean energy, Genome, 03 medical and health sciences, Andropogoneae, Polyploid, Saccharum officinarum, Ploidy, Gene, 030304 developmental biology, 010606 plant biology & botany, Synteny
Abstract

Modern sugarcane (Saccharum spp.) is an important grass that contributes 60% of the raw sugar produced worldwide and has a high biofuel production potential. It was created about a century ago through hybridization of two highly polyploid species, namely S. officinarum and S. spontaneum. We investigated genome dynamics in this highly polyploid context by analyzing two homoeologous sequences (97 and 126 kb) in a region that has already been studied in several cereals. Our findings indicate that the two Saccharum species diverged 1.5-2 million years ago from one another and 8-9 million years ago from sorghum. The two sugarcane homoeologous haplotypes show perfect colinearity as well as high gene structure conservation. Apart from the insertion of a few retrotransposable elements, high homology was also observed for the non-transcribed regions. Relative to sorghum, the sugarcane sequences displayed colinearity, with the exception of two genes present only in sorghum, and striking homology in most non-coding parts of the genome. The gene distribution highlighted high synteny and colinearity with rice, and partial colinearity with each homoeologous maize region, which became perfect when the sequences were combined. The haplotypes observed in sugarcane may thus closely represent the ancestral Andropogoneae haplotype. This analysis of sugarcane haplotype organization at the sequence level suggests that the high ploidy in sugarcane did not induce generalized reshaping of its genome, thus challenging the idea that polyploidy quickly induces generalized rearrangement of genomes. These results also confirm the view that sorghum is the model of choice for sugarcane.

Published
2007
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15. Morgane, a new LTR retrotransposon group, and its subfamilies in wheats

Author

François Sabot, Michel Bernard, Pierre Sourdille, Nathalie Chantret, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques, Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques (UMR PIA-GACA), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Montpellier (ENSA M)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Transposable element, Subfamily, DNA, Plant, Retroelements, Molecular Sequence Data, WHEAT, Retrotransposon, SEQUENCE REPETEE TERMINALE, Plant Science, Biology, Poaceae, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, GRASS, 03 medical and health sciences, Group (periodic table), Sequence Homology, Nucleic Acid, Genetics, Triticeae, Triticum, 030304 developmental biology, Expressed Sequence Tags, 2. Zero hunger, 0303 health sciences, Base Sequence, Models, Genetic, Terminal Repeat Sequences, food and beverages, General Medicine, GENETIQUE, Biotic stress, biology.organism_classification, EVOLUTION, humanities, Sequence identity, GENOME, Insect Science, TRANSPOSABLE ELEMENTS, Animal Science and Zoology, Genome, Plant, 010606 plant biology & botany
Abstract

Transposable elements are the main components of grass genomes, especially in Triticeae species. In a previous analysis, we identified a very short element, Morgane_CR626934-1; here we describe more precisely this unusual element. Morgane_CR626934-1 shows high sequence identity (until 98%) with ESTs belonging to other possible small elements, expressed under abiotic and biotic stress conditions. No putative functional polyprotein could be identified in all of these different Morgane-like sequences. Moreover, elements from the Morgane_CR626934-1 subfamily are found only in wheats and Agropyrum genomes and among these species, only Ae. tauschii and T. aestivum present a high copy number of these elements. They are highly conserved in wheat genomes (95.5%). Based on the uncommon characteristics of the described Morgane-like elements, we proposed to classify them in a new group within the Class I LTR retrotransposon, the Morgane group.

Published
2006
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16. PCR identification of durum wheat BAC clones containing genes coding for carotenoid biosynthesis enzymes and their chromosome localization

Author

Jorge Dubcovsky, S Somma, Alberto Cenci, Antonio Blanco, and Nathalie Chantret

Subjects
Crop and Pasture Production, Chromosomes, Artificial, Bacterial, Agricultural Biotechnology, Plant Biology & Botany, Biology, Carotenoid biosynthesis, Chromosomes, Chromosomes, Plant, Endosperm, wheat, Genetics, Molecular Biology, Gene, Carotenoid, Triticum, BAC, DNA Primers, chemistry.chemical_classification, Genome, Alkyl and Aryl Transferases, Chromosome localization, Bacterial, Chromosome Mapping, food and beverages, Plant, General Medicine, Carotenoids, Enzyme, chemistry, Geranylgeranyl-Diphosphate Geranylgeranyltransferase, Artificial, Oxidoreductases, carotenoid biosynthesis, Genome, Plant, Biotechnology
Abstract

Carotenoids are essential components in all plants. Their accumulation in wheat seed determines the endosperm colour, which is an important quality trait in wheat. In this study, we report the isolation of BAC clones containing genes coding for three different enzymes of the carotenoid biosynthesis pathway: phytoene synthase (PSY), phytoene desaturase (PDS), and ζ-carotene desaturase (ZDS). Primers were designed on the basis of wheat ESTs similar to the sequences of these three genes in other species, and used to screen a BAC library from Triticum turgidum var. durum (2n = 28, genomes AABB). Eight, six, and nine 384-well plates containing at least one positive clone were found for PSY, PDS, and ZDS, respectively. BACs selected for each of these genes were then divided in two groups corresponding to the A and B genomes of tetraploid wheat, based on differences in the length of the PCR amplification products, conformation-sensitive gel electrophoresis (CSGE), or cleavage amplification polymorphisms. Positive clones were then assigned to chromosomes using a set of D genome substitution lines in T. turgidum var. durum 'Langdon'. PSY clones were localized on chromosomes 5A and 5B, PDS on chromosomes 4A and 4B, and ZDS on chromosomes 2A and 2B. The strategies used for the PCR screening of large BAC libraries and for the differentiation of BAC clones from different genomes in a polyploid species are discussed.Key words: wheat, carotenoid biosynthesis, BAC.

Published
2004
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17. High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches

Author

Marie-Laure Pilet-Nayel, Hélène Navier, Ahmed Hajri, Joëlle Ronfort, Maxime Bonhomme, Christophe Jacquet, Concetta Burgarella, Peter Tiffin, Frédéric Debellé, Henri Miteul, Alain Baranger, Joann Mudge, Roman Briskine, Nathalie Chantret, Olivier André, Jean Marie Prosperi, Yacine Badis, Bernard Dumas, Nevin D. Young, 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, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Department of Computer Science and Engineering, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, National Center for Genome Resources, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Department of Plant Biology, CNRS, Universite Paul Sabatier, INRA, French Agence Nationale de la Recherche [ANR-10-GENM-0007], US National Science Foundation [IOS-1237993], NGCR, Evolution des Interactions Plantes-Microorganismes, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), University of Minnesota [Twin Cities] (UMN), National center for genome resources (NCGR), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Interactions Microbiennes dans la Rhizosphère et les Racines, ANR-10-GENM-0007,Immunit-Ae,Diversité des composants génétiques et des mécanismes de résistance à Aphanomyces euteiches chez les légumineuses.(2010), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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 la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST

Subjects
Candidate gene, Genome-wide association study, F-box protein, Cytokinins, Transcription, Genetic, Physiology, health care facilities, manpower, and services, [SDV]Life Sciences [q-bio], education, Colony Count, Microbial, Single-nucleotide polymorphism, Locus (genetics), partial resistance, Ralstonia, Plant Science, Aphanomyces, Quantitative trait locus, Genes, Plant, Aphanomyces euteiches, Gene Expression Regulation, Plant, Medicago truncatula, oomycete, RNA, Messenger, Gene, health care economics and organizations, Disease Resistance, Plant Diseases, Plant Proteins, Genetics, biology, F-Box Proteins, Chromosome Mapping, biology.organism_classification, root, Up-Regulation, Mutation, Root Nodules, Plant, Signal Transduction, Transcription Factors
Abstract

Summary � The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume. � A high-density (� 5.1 million single nucleotide polymorphisms (SNPs)) genome-wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines. � GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus (r 2 = 23%) were in the promoter and coding regions of an F-box protein coding gene. Subsequent qRT-PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F-box protein rather than gene expression. � These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.

Published
2014
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18. Impact of recurrent gene duplication on adaptation of plant genomes

Author

Iris Fischer, Jean-François Dufayard, Sylvain Glémin, Jacques Dainat, Vincent Ranwez, Nathalie Chantret, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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 de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), French Agence Nationale de la Recherche [ANR-11-BSV7-013-03], French Agence Nationale de la Recherche Investissements d'avenir/Bioinformatique [ANR-10-BINF-01-02], 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), 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), ANR-11-BSV7-0013,TRANS,Les transitions de systèmes de reproduction chez les angiosperms et leurs conséquences génomiques(2011), ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Time Factors, Gene duplication, Ultraparalogs (UP), 2R hypothesis, Évolution, Plant Science, adaptation, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Negative selection, Databases, Genetic, Cluster Analysis, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Sélection individuelle, Genetics, 0303 health sciences, Superorthologs (SO), F70 - Taxonomie végétale et phytogéographie, Adaptation, Physiological, Positive selection, Multigene Family, Gene retention, Empreinte ADN, Genome, Plant, Research Article, Genome evolution, Séquence nucléotidique, F60 - Physiologie et biochimie végétale, Biology, Magnoliophyta, 03 medical and health sciences, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Adaptation, Codon, Gene, Selection (genetic algorithm), réplication, 030304 developmental biology, Comparative genomics, Génome, Polymorphism, Genetic, Molecular Sequence Annotation, Lineage specific expansion (LSE), Amélioration des plantes, Gène, Mutation, 010606 plant biology & botany
Abstract

Publis014-agap-018; Background: Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale.[br/]Results: We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework. We found 5.38% of alignments in LSE genes with codons under positive selection. In contrast, we found no evidence for codons under positive selection in the single-copy reference set. An analysis at the branch level shows that purifying selection acted more strongly on single-copy genes than on LSE gene clusters. Moreover we detect significantly more branches indicating evolution under positive selection and/or relaxed constraint in LSE genes than in single-copy genes.[br/]Conclusions: In this – to our knowledge –first genome-scale study we provide strong empirical support for the hypothesis that LSE genes fuel adaptation in angiosperms. Our conservative approach for detecting selection footprints as well as our results can be of interest for further studies on (plant) gene family evolution.

Published
2014
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19. Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula

Author

Karine Loridon, Jérôme Gouzy, Nathalie Chantret, Frédéric Martins, Jean-Marie Prosperi, Concetta Burgarella, Joëlle Ronfort, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Plateforme GeT (Génome et Transcriptome), Génopole Toulouse, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-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 la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Toulouse III - Paul Sabatier (UT3), and 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)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Genotype, Population, Molecular Sequence Data, Single-nucleotide polymorphism, 01 natural sciences, Genome, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, 03 medical and health sciences, Gene Frequency, Medicago truncatula, Genetics, selfing, SNP, education, Allele frequency, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, DNA Primers, Demography, 0303 health sciences, education.field_of_study, Genetic diversity, biology, Base Sequence, Mediterranean Region, sequence diversity, food and beverages, Genetic Variation, Sequence Analysis, DNA, single-nucleotide polymorphism, biology.organism_classification, ascertainment bias, Genome, Plant, 010606 plant biology & botany, Biotechnology
Abstract

Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency

Published
2013
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20. Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.)

Author

Nathalie Chantret, Isabelle Hochu, Audrey Weber, Stéphane De Mita, Thomas Bataillon, Joan Ho-Huu, Joëlle Ronfort, 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), INRA, ARCAD, Agropolis Foundation, 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), and Chantret, Nathalie

Subjects
0106 biological sciences, Duplication, Neofunctionalization, Evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Paralogous Gene, Biology, 01 natural sciences, Paralogs evolution, 03 medical and health sciences, Negative selection, Gene Duplication, Subfunctionalization, Gene duplication, Medicago, QH359-425, Selection, Genetic, Gene, Ecology, Evolution, Behavior and Systematics, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, Membrane Transport Proteins, Polygalacturonase, Evolutionary biology, Synonymous substitution, Functional divergence, Research Article, 010606 plant biology & botany
Abstract

Background Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies. Results Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication. Conclusions This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.

Published
2012
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21. Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species

Author

Arnaud Bellec, Pierre Sourdille, Philippe Leroy, Jérôme Salse, Carole Dossat, Jean Weissenbach, Bastien Laubin, Ivan Dubois, Michel Bernard, Laurence Cattolico, Marie-Françoise Gautier, Nathalie Chantret, Philippe Joudrier, Michel Caboche, Sébastien Aubourg, François Sabot, Michel Beckert, Boulos Chalhoub, Diversité et adaptation des plantes cultivées (UMR DIAPC), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), UMR 1097 Diversité et Adaptation des Plantes Cultivées, Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-MontpellierSupAgro (MontpellierSupAgro)-Génétique et amélioration des plantes (G.A.P.)-Diversité et Adaptation des Plantes Cultivées (DIA-PC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
0106 biological sciences, Chromosomes, Artificial, Bacterial, Molecular Sequence Data, Locus (genetics), Biology, CARTOGRAPHIE GENETIQUE, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Genetics, Coding region, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Codon, Molecular clock, Molecular Biology, Gene, Conserved Sequence, Triticum, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, Comparative genomics, 0303 health sciences, Base Sequence, food and beverages, Hordeum, Oryza, Introns, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], DNA, Intergenic, RIZ, 010606 plant biology & botany
Abstract

UMR DIAPC, UMR DAP équipe DGB; We study here the evolution of genes located in the same physical locus using the recently sequenced Ha locus in seven wheat genomes in diploid, tetraploid, and hexaploid species and compared them with barley and rice orthologous regions. We investigated both the conservation of microcolinearity and the molecular evolution of genes, including coding and noncoding sequences. Microcolinearity is restricted to two groups of genes (Unknown gene-2, VAMP, BGGP, Gsp-1, and Unknown gene-8 surrounded by several copies of ATPase), almost conserved in rice and barley, but in a different relative position. Highly conserved genes between wheat and rice run along with genes harboring different copy numbers and highly variable sequences between close wheat genomes. The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases

Published
2008
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22. Genome-wide analysis of the rice and arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining

Author

Marie Francoise Gautier, Freddy Boutrot, Nathalie Chantret, 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), John Innes Centre, The Sainsbury Laboratory [Norwich] (TSL), Diversité et adaptation des plantes cultivées (UMR DIAPC), and 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)

Subjects
0106 biological sciences, Arabidopsis, UniGene, 01 natural sciences, Databases, Genetic, Arabidopsis thaliana, Phylogeny, Triticum, Plant Proteins, 2. Zero hunger, Genetics, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, food and beverages, Genomics, analyse comparative, Tandem Repeat Sequences, Multigene Family, Tandem exon duplication, Genome, Plant, Biotechnology, Research Article, lcsh:QH426-470, lcsh:Biotechnology, Molecular Sequence Data, RIZ, CARTOGRAPHIE GENETIQUE, BIOLOGIE DU DEVELOPPEMENT, PROTEINE DE TRANSFERT DES LIPIDES, Biology, Genes, Plant, 03 medical and health sciences, blé, Species Specificity, lcsh:TP248.13-248.65, phylogénie, Gene family, grande culture, Amino Acid Sequence, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Oryza sativa, Sequence Homology, Amino Acid, Arabidopsis Proteins, Genetic Variation, Oryza, biology.organism_classification, lcsh:Genetics, oryza sativa, Carrier Proteins, 010606 plant biology & botany
Abstract

Background Plant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. Our objective was to characterize the complete nsLtp gene family in rice and arabidopsis and to perform wheat EST database mining for nsLtp gene discovery. Results In this study, we carried out a genome-wide analysis of nsLtp gene families in Oryza sativa and Arabidopsis thaliana and identified 52 rice nsLtp genes and 49 arabidopsis nsLtp genes. Here we present a complete overview of the genes and deduced protein features. Tandem duplication repeats, which represent 26 out of the 52 rice nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes identified, support the complexity of the nsLtp gene families in these species. Phylogenetic analysis revealed that rice and arabidopsis nsLTPs are clustered in nine different clades. In addition, we performed comparative analysis of rice nsLtp genes and wheat (Triticum aestivum) EST sequences indexed in the UniGene database. We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar. The 122 wheat non-redundant nsLTPs were organized in eight types and 33 subfamilies. Based on the observation that seven of these clades were present in arabidopsis, rice and wheat, we conclude that the major functional diversification within the nsLTP family predated the monocot/dicot divergence. In contrast, there is no type VII nsLTPs in arabidopsis and type IX nsLTPs were only identified in arabidopsis. The reason for the larger number of nsLtp genes in wheat may simply be due to the hexaploid state of wheat but may also reflect extensive duplication of gene clusters as observed on rice chromosomes 11 and 12 and arabidopsis chromosome 5. Conclusion Our current study provides fundamental information on the organization of the rice, arabidopsis and wheat nsLtp gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat nsLtp gene families and will strongly support further transcript profiling or functional analyses of nsLtp genes. Until such time as specific physiological functions are defined, it seems relevant to categorize plant nsLTPs on the basis of sequence similarity and/or phylogenetic clustering.

Published
2008
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23. Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome

Author

Nazeema, Jannoo, Laurent, Grivet, Nathalie, Chantret, Olivier, Garsmeur, Jean Christophe, Glaszmann, Paulo, Arruda, and Angélique, D'Hont

Subjects
Expressed Sequence Tags, Polyploidy, Chromosomes, Artificial, Bacterial, DNA, Plant, Molecular Sequence Data, Genes, Plant, Poaceae, Saccharum
Abstract

Modern sugarcane (Saccharum spp.) is an important grass that contributes 60% of the raw sugar produced worldwide and has a high biofuel production potential. It was created about a century ago through hybridization of two highly polyploid species, namely S. officinarum and S. spontaneum. We investigated genome dynamics in this highly polyploid context by analyzing two homoeologous sequences (97 and 126 kb) in a region that has already been studied in several cereals. Our findings indicate that the two Saccharum species diverged 1.5-2 million years ago from one another and 8-9 million years ago from sorghum. The two sugarcane homoeologous haplotypes show perfect colinearity as well as high gene structure conservation. Apart from the insertion of a few retrotransposable elements, high homology was also observed for the non-transcribed regions. Relative to sorghum, the sugarcane sequences displayed colinearity, with the exception of two genes present only in sorghum, and striking homology in most non-coding parts of the genome. The gene distribution highlighted high synteny and colinearity with rice, and partial colinearity with each homoeologous maize region, which became perfect when the sequences were combined. The haplotypes observed in sugarcane may thus closely represent the ancestral Andropogoneae haplotype. This analysis of sugarcane haplotype organization at the sequence level suggests that the high ploidy in sugarcane did not induce generalized reshaping of its genome, thus challenging the idea that polyploidy quickly induces generalized rearrangement of genomes. These results also confirm the view that sorghum is the model of choice for sugarcane.

Published
2007

24. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations

Author

Michel Bernard, Philippe Leroy, Thomas Wicker, Pierre Sourdille, François Sabot, Bastien Laubin, Nathalie Chantret, Romain Guyot, Boulos Chalhoub, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Plant Biology, Universität Zürich [Zürich] (UZH), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques, Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Universität Zürich [Zürich] = University of Zurich (UZH), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques (UMR PIA-GACA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Montpellier (ENSA M), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Transposable element, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genome evolution, DNA, Plant, Retrotransposon, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Species Specificity, Polyploid, Genetics, Triticeae, Molecular Biology, Triticum, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, food and beverages, Hordeum, Sequence Analysis, DNA, General Medicine, GENETIQUE, biology.organism_classification, Long terminal repeat, DNA Transposable Elements, Ploidy, Edible Grain, Genome, Plant, 010606 plant biology & botany
Abstract

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.

Published
2005
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25. Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice

Author

Olin D. Anderson, François Sabot, Jorge Dubcovsky, Nathalie Chantret, and Alberto Cenci

Subjects
Grain Softness Protein, Chromosomes, Artificial, Bacterial, puroindoline, DNA, Plant, Sequence analysis, Plant Biology & Botany, Molecular Sequence Data, Sequence Homology, Plant Biology, Locus (genetics), Biology, Genes, Plant, Genome, Chromosomes, Chromosomes, Plant, Chromosome regions, Gene density, wheat, Genetics, Amino Acid Sequence, Molecular Biology, Gene, Chromosome 12, Triticum, Plant Proteins, Genetics & Heredity, Sequence Homology, Amino Acid, Bacterial, Chromosome, food and beverages, microcolinearity, Oryza, General Medicine, Plant, DNA, Sequence Analysis, DNA, hardness, Interspersed Repetitive Sequences, Amino Acid, Genes, Artificial, Sequence Analysis, Genome, Plant
Abstract

The Hardness (Ha) locus on chromosome 5D is the main determinant of grain texture in hexaploid wheat. The related genes Puroindoline-a and -b (Pina-D1, Pinb-D1) and Grain Softness Protein (Gsp-D1) are tightly linked at this locus. Mutations in the Pina-D1 and Pinb-D1 genes are associated with increased grain hardness. We report here the complete sequence of a 101-kb BAC clone from Triticum monococcum (Am genome) which includes these three genes, and its comparison with the orthologous region in rice. The genes Gsp-A m1, Pina-A m1 and Pinb-A m1 are separated by 37 kb and 32 kb, respectively, and are organized in the same transcriptional orientation. Four additional genes, including a pair of duplicated genes, were identified upstream of Gsp-A m1 within a high-density gene island. These additional genes were found in the same order and orientation, and the same relative distances apart as similar genes previously annotated on rice chromosome 12. An interesting discovery was a small unannotated putative rice gene that was similar to the Gsp-A m1 gene of T. monococcum (65% similarity at the protein level), and that was disposed in the same orientation, and located in the same position relative to the other orthologous genes. The high gene density observed in this BAC (1 gene per 14 kb) was expected for a distal chromosome region, but the level of microcolinearity with rice was higher than that reported in similar distal regions of other wheat chromosomes. Most of the BAC sequence (40%) was represented by repetitive elements, mainly concentrated in regions adjacent to the genes Pina-A m 1 and Pinb-A m 1. Rearrangements among these repetitive elements might provide an explanation for the frequent deletions observed at this locus in the genomes of the polyploid wheat species. © Springer-Verlag 2004.

Published
2003
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26. Mapping QTL involved in adult plant resistance to powdery mildew in the winter wheat line RE714 in two susceptible genetic backgrounds

Author

Noureddine Boukhatem, JM Jacquemin, G. Doussinault, Nathalie Chantret, D Mingeot, A. Dekeyser, Philippe Baret, Pierre Sourdille, UMR 0118 UMR INRA / ENSAR : Amélioration des Plantes et de Biotechnologies Végétales, Institut National de la Recherche Agronomique (INRA)-Génétique et amélioration des plantes (G.A.P.)-UMR INRA / ENSAR : Amélioration des Plantes et de Biotechnologies Végétales (RENN UMR ADPBV), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and ProdInra, Archive Ouverte

Subjects
0106 biological sciences, Genetics, 0303 health sciences, food and beverages, Locus (genetics), Plant Science, Plant disease resistance, Biology, Quantitative trait locus, GENETIQUE, 01 natural sciences, Genetic determinism, 03 medical and health sciences, Gene mapping, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Poaceae, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science, Gene, Powdery mildew, 030304 developmental biology, 010606 plant biology & botany
Abstract

The objective was to study the genetic basis of adult plant resistance to powdery mildew of the winter wheat line RE714 by quantitative trait loci (QTL) analysis and to investigate the stability of the QTL detected in two different genetic backgrounds. Two DH populations from the crosses between RE714 and the susceptible parents 'Festin' and 'Hardi' were used. Reaction of the DH lines to powdery mildew was assessed in different environments in Belgium under natural disease infection. Considering both populations and according to the environment tested, one to seven QTL were detected. Among them, residual effects of the race-specific resistance genes Pm4b and MIRE were found, Two major QTL were very stable (on chromosome 5D and at the MlRE locus), since them were detected in both populations and over all environments tested. The QTL detected varied according to the susceptible parent used. and a residual effect at the Pm4b gene was not observed with the genetic background of 'Hardi'.

Published
2002

27. A major QTL for powdery mildew resistance is stable over time and at two development stages in winter wheat

Author

JM Jacquemin, G. Doussinault, Nathalie Chantret, Pierre Sourdille, Michel Bernard, D Mingeot, UMR 0118 UMR INRA / ENSAR : Amélioration des Plantes et de Biotechnologies Végétales, Institut National de la Recherche Agronomique (INRA)-Génétique et amélioration des plantes (G.A.P.)-UMR INRA / ENSAR : Amélioration des Plantes et de Biotechnologies Végétales (RENN UMR ADPBV), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), ProdInra, Archive Ouverte, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Population, [SDV.GEN] Life Sciences [q-bio]/Genetics, Quantitative trait locus, Biology, Plant disease resistance, CARTOGRAPHIE GENETIQUE, 01 natural sciences, 03 medical and health sciences, Genetics, Poaceae, education, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Resistance (ecology), food and beverages, Chromosome, General Medicine, AMELIORATION DES PLANTES, GENETIQUE, biology.organism_classification, Agronomy, Seedling, Agronomy and Crop Science, Powdery mildew, 010606 plant biology & botany, Biotechnology
Abstract

Despite the large impact of powdery mildew in wheat cultivated areas, little has been done to study powdery mildew resistance by QTL analysis up to now. The objective of the present paper is to present how the genetic basis of powdery mildew resistance in the resistant wheat line RE714 have been studied by QTL analysis at the adult plant stage over the course of 3 years, and at the vernalized seedling plant stage, and a comparison between the results obtained. Two segregating populations (DH and F2:3) were derived from the cross between the resistant line (RE714), and a susceptible line (Hardi); these were analysed for powdery mildew resistance at the adult plant stage in the field under natural infection conditions in 1996, 1997 and 1998. The DH population was also tested for powdery mildew resistance at the vernalized seedling stage with four different isolates of powdery mildew. At the adult plant stage, a total of three QTLs (on chromosomes 5D, 4A and 6A) and five QTLs (on chromosomes 5D, 6A, 7A and 7B) were found for the DH and F2:3 populations, respectively. The genetic control of resistance was found to be polygenic but involved a major QTL (on chromosome 5D), which was detected each year and which explained a high proportion of the variability observed (28.1%–37.9%). At the vernalized seedling stage, two QTLs were found (on chromosomes 5D and 7B) and the QTL detected on chromosome 5D was common to the four isolates tested. The comparison between the two development stages showed that the QTL on chromosome 5D was detected in all the different environments tested and again explained a high proportion of the variability. Different molecular interpretations of this QTL have also been discussed.

Published
2001

28. Location and mapping of the powdery mildew resistance gene MIRE and detection of a resistance QTL by bulked segregant analysis (BSA) with microsatellites in wheat

Author

G. Doussinault, Pierre Sourdille, M. Tavaud, Michel Bernard, Marion S. Röder, Nathalie Chantret, UMR 0118 UMR INRA / ENSAR : Génétique et amélioration des plantes, Institut National de la Recherche Agronomique (INRA)-Génétique et amélioration des plantes (G.A.P.)-UMR INRA / ENSAR : Génétique et amélioration des plantes (RENN UMR GENET AMELIOR PLANTES), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, disease resistance, molecular markers, Population, Triticum aestivum, Blumeria graminis, Quantitative trait locus, Biology, Plant disease resistance, 01 natural sciences, 03 medical and health sciences, Genetics, education, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, QT mapping, Bulked segregant analysis, food and beverages, General Medicine, GENETIQUE, biology.organism_classification, Genetic marker, Microsatellite, Agronomy and Crop Science, Powdery mildew, 010606 plant biology & botany, Biotechnology, Blumeria graminis f. sp.tritici
Abstract

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat (Triticum aestivum). The objective of this study was to locate and map a recently identified powdery mildew resistance gene, MlRE, carried by the resistant line RE714 using microsatellites uniformly distributed among the whole genome together with a bulked segregant analysis (BSA). The bulks consisted of individuals with an extreme phenotype taken from a population of 140 F-3 families issued from the cross between RE714 (resistant) and Hardi (susceptible). The population had been tested with three powdery mildew isolates at the seedling stage. Qualitative interpretation of the resistance tests located the MlRE gene on the distal part of the long arm of chromosome 6A. A subsequent quantitative interpretation of the resistance permitted us to detect another resistance factor on a linkage group assigned to chromosome 5D, which was constructed with microsatellites for which a polymorphism of intensity between bulks was observed. This quantitative trait locus (QTL) explained 16.8-25.34% of the total variation. An interaction between both the resistant factor (MlRE and the QTL) was found for only one of the isolates tested. This study shows the advantage of making a quantitative interpretation of resistant tests and that the use of microsatellites combined with BSA is a powerful strategy to locate resistance genes in wheat.

Published
2000
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29. Genome-wide analysis of the rice and arabidopsis () gene families and identification of wheat genes by EST data mining-4

Author

Freddy Boutrot, Nathalie Chantret, Marie-Françoise Gautier, Freddy Boutrot, Nathalie Chantret, and Marie-Françoise Gautier

Abstract

E 49 arabidopsis nsLTPs and the 156 wheat nsLTPs presented in Table 1, Table 2, and Additional file , respectively. AtLTPII.8 that appears to be more distantly related to other type II sequences (see the phylogenetic analysis) was excluded. The values allowing direct identification of the nsLTP type are grey boxed. cysteine residue number 6 is missing in AtLTPII.10. cysteine residue number 7 is missing in TaLTPVIa.5. cysteine residue number 8 is missing in AtLTPI.1. AtLTPII.10, OsLTPVI.1, OsLTPVI.2, OsLTPVI.4, and TaLTPVIa subfamily members harbor an extra cysteine residue. All type VI contain a Val 4 aa before Cys7 and a Met 10 aa before Cys7 allowing a distinction between type IV and type VI. AtLTPII.6 harbors an extra cysteine residue. TaLTPIVc.1 and TaLTPIVa subfamily members harbor an extra cysteine residue. 12 amino acid residues were counted for the TaLTPIVd.1 that displays no CXC motif. OsLTPVII.1 and TaLTPVIIa.1 subfamily members harbor an extra cysteine residue.Copyright information:Taken from "Genome-wide analysis of the rice and arabidopsis () gene families and identification of wheat genes by EST data mining"http://www.biomedcentral.com/1471-2164/9/86BMC Genomics 2008;9():86-86.Published online 21 Feb 2008PMCID:PMC2277411.

Published
2011
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30. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

Author

François Sabot, Romain Guyot, Thomas Wicker, Nathalie Chantret, Bastien Laubin, Boulos Chalhoub, Philippe Leroy, Pierre Sourdille, and Michel Bernard

Abstract

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed. [ABSTRACT FROM AUTHOR]

Published
2005
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31. Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

Author

Thomas Bataillon, Karine Loridon, Joëlle Ronfort, Nathalie Chantret, and Stéphane De Mita

Subjects
Genotype, Evolution, Population, Molecular Sequence Data, Biology, Nucleotide diversity, Evolution, Molecular, Negative selection, Botany, Genetic variation, Medicago truncatula, QH359-425, Selection, Genetic, education, Symbiosis, Gene, Ecology, Evolution, Behavior and Systematics, Plant Proteins, education.field_of_study, Natural selection, Polymorphism, Genetic, fungi, Genetic Variation, food and beverages, Phenotypic trait, biology.organism_classification, Adaptation, Physiological, Evolutionary biology, Rhizobium, Research Article
Abstract

Background We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways. Results We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection. Conclusion We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be detected at different time scales in both flowering and symbiotic pathways.

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