Article thumbnail

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

By 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 and Manuel Ruiz

Abstract

We produced a unique large dataset 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 dataset 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/

Topics: rna sequence, genomes, wild plants, plant genetic resources, mapping, secuencia de arn, genomas, plantas silvestres, recursos genéticos vegetales
Publisher: 'Wiley'
Year: 2016
DOI identifier: 10.1111/1755-0998.12587
OAI identifier: oai:cgspace.cgiar.org:10568/76382
Provided by: CGSpace
Journal:
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • https://hdl.handle.net/10568/7... (external link)
  • https://doi.org/10.1111/1755-0... (external link)

  • To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

    Suggested articles