title: Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery.
abstract: The alpine plant Arabis 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 Arabidopsis 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 Arabis alpina, thus constituting an important resource for future ecological genomic studies.
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Joseph Fourier, UMR-CNRS 5553, BP53 38041, Grenoble, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Lobréaux
authors.forename: Stephanie
authors.initials: S
authors.lastname: Manel
authors.forename: Christelle
authors.initials: C
authors.lastname: Melodelima
mesh_terms: D031214:Arabis / Q000145:classification* / Q000235:genetics*; D023281:Genomics; D060005:Genotyping Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Alpine rock-cress; alpine plant; genetic diversity; genomic assembly; single-nucleotide polymorphisms