title: A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.
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/.
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Gautier
authors.initials: G
authors.lastname: Sarah
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Felix
authors.initials: F
authors.lastname: Homa
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Pointet
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Sandy
authors.initials: S
authors.lastname: Contreras
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: François
authors.initials: F
authors.lastname: Sabot
authors.affiliation: Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: Nabholz
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Santoni
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Sauné
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Ardisson
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Chantret
authors.affiliation: INRA, UR1052, GAFL, 67 allée des Chênes Domaine Saint Maurice- CS60094, 84143, Montfavet Cedex, France.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sauvage
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: James
authors.initials: J
authors.lastname: Tregear
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Jourda
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: David
authors.initials: D
authors.lastname: Pot
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Vigouroux
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Hana
authors.initials: H
authors.lastname: Chair
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: Nora
authors.initials: N
authors.lastname: Scarcelli
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Billot
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Nabila
authors.initials: N
authors.lastname: Yahiaoui
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Roberto
authors.initials: R
authors.lastname: Bacilieri
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Bouchaib
authors.initials: B
authors.lastname: Khadari
authors.affiliation: CIRAD/CRC, UMR AGAP, UWI, St Augustine, Trinidad and Tobago.
authors.forename: Michel
authors.initials: M
authors.lastname: Boccara
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: Adéline
authors.initials: A
authors.lastname: Barnaud
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Péros
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Labouisse
authors.affiliation: UMR IRD-UM2-CIRAD DIADE, IRD, Montpellier, France.
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Pham
authors.affiliation: Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: David
authors.affiliation: Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Glémin
authors.affiliation: CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.|CIAT, Recta Cali Palmira km 17, Cali, Colombia.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ruiz
mesh_terms: D005075:Biological Evolution; D020451:Contig Mapping; D018556:Crops, Agricultural / Q000235:genetics*; D018745:Genome, Plant; D056186:Metagenomics; D059467:Transcriptome
keywords: RNA-Seq; comparative genomics; reference transcriptomes