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Development of an A rabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery
Author(s) -
Lobréaux Stéphane,
Manel Stephanie,
Melodelima Christelle
Publication year - 2014
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12189
Subject(s) - contig , biology , genome , gene , sequence assembly , genetics , computational biology , dna sequencing , whole genome sequencing , transcriptome , gene expression
Abstract The alpine plant A rabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A . alpina genomic fragments using next‐generation sequencing technologies. These contigs cover 172 Mb of the A . alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative A rabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A . thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127 041 single‐nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of A rabis alpina, thus constituting an important resource for future ecological genomic studies.