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

Sarah Gautier, Homa Félix, Pointet Stéphanie, Contreras Sandy, Sabot François, Nabholz Benoit, Santoni Sylvain, Sauné Laure, Ardisson Morgane, Chantret Nathalie, Sauvage Christopher, Tregear James, Jourda Cyril, Pot David, Vigouroux Yves, Chaïr Hâna, Scarcelli Nora, Billot Claire, Yahiaoui Nabila, Bacilieri Roberto, Khadari Bouchaib, Boccara Michel, Barnaud Adeline, Péros Jean-Pierre, Labouisse Jean-Pierre, Pham Jean Louis, David Jacques, Glemin Sylvain, Ruiz Manuel. 2017. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources, 17 (3) : pp. 565-580.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Url - jeu de données : http://arcad-bioinformatics.southgreen.fr/ / Url - jeu de données : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA326055 / Url - jeu de données : https://github.com/SouthGreenPlatform/arcad-hts

Quartile : Outlier, Sujet : ECOLOGY / Quartile : Q1, Sujet : EVOLUTIONARY BIOLOGY / Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

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. (Résumé d'auteur)

Mots-clés Agrovoc : Transcription génique, Séquence nucléotidique, ARN, génomique, Génétique des populations, Plante sauvage, Plante de culture, Dioscorea, Pennisetum glaucum, Digitaria exilis, Évolution, Domestication des plantes

Mots-clés libres : Reference transcriptomes, RNA-seq, Comparative genomics

Classification Agris : F70 - Plant taxonomy and geography
F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Sarah Gautier, INRA (FRA)
  • Homa Félix
  • Pointet Stéphanie, CIRAD-BIOS-UMR AGAP (FRA)
  • Contreras Sandy, INRA (FRA)
  • Sabot François, IRD (FRA)
  • Nabholz Benoit, ISEM (FRA)
  • Santoni Sylvain, INRA (FRA)
  • Sauné Laure, INRA (FRA)
  • Ardisson Morgane, INRA (FRA)
  • Chantret Nathalie, INRA (FRA)
  • Sauvage Christopher, INRA (FRA)
  • Tregear James, IRD (FRA)
  • Jourda Cyril, CIRAD-BIOS-UMR PVBMT (REU)
  • Pot David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6144-8448
  • Vigouroux Yves, IRD (FRA)
  • Chaïr Hâna, CIRAD-BIOS-UMR AGAP (FRA)
  • Scarcelli Nora, IRD (FRA)
  • Billot Claire, CIRAD-BIOS-UMR AGAP (FRA)
  • Yahiaoui Nabila, CIRAD-BIOS-UMR AGAP (FRA)
  • Bacilieri Roberto, INRA (FRA)
  • Khadari Bouchaib, INRA (FRA)
  • Boccara Michel, CIRAD-BIOS-UMR AGAP (TTO)
  • Barnaud Adeline, IRD (FRA)
  • Péros Jean-Pierre, INRA (FRA)
  • Labouisse Jean-Pierre, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5592-6789
  • Pham Jean Louis, IRD (FRA)
  • David Jacques, Montpellier SupAgro (FRA)
  • Glemin Sylvain, ISEM (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (COL) ORCID: 0000-0001-8153-276X

Source : Cirad-Agritrop (https://agritrop.cirad.fr/581322/)

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