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 paper 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 analyzed and 127,041 Single Nucleotide Polymorphisms identified. This contig dataset will contribute to improving understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.
variant pileup for sample 2 reads mapping
Paired end reads from sample 2 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample2_pileup_var.txt.bz2
variant pileup for sample 1 reads mapping
Paired end reads from sample 1 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtained with samtools from bam file.
sample1_pileup_var.txt.bz2
variant pileup for sample 3 reads mapping
Paired end reads from sample 3 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample3_pileup_var.txt.bz2
variant pileup for sample 4 reads mapping
Paired end reads from sample 4 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample4_pileup_var.txt.bz2
variant pileup for sample 5 reads mapping
Paired end reads from sample 5 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample5_pileup_var.txt.bz2
variant pileup for sample 6 reads mapping
Paired end reads from sample 6 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample6_pileup_var.txt.bz2
variant pileup for sample 7 reads mapping
Paired end reads from sample 7 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample7_pileup_var.txt.bz2
variant pileup for sample 8 reads mapping
Paired end reads from sample 8 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample8_pileup_var.txt.bz2
variant pileup for sample 9 reads mapping
Paired end reads from sample 9 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample9_pileup_var.txt.bz2
variant pileup for sample 10 reads mapping
Paired end reads from sample 10 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample10_pileup_var.txt.bz2
variant pileup for sample 11 reads mapping
Paired end reads from sample 11 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample11_pileup_var.txt.bz2
variant pileup for sample 12 reads mapping
Paired end reads from sample 12 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample12_pileup_var.txt.bz2
variant pileup for sample 13 reads mapping
Paired end reads from sample 13 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample13_pileup_var.txt.bz2
variant pileup for sample 14 reads mapping
Paired end reads from sample 14 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample14_pileup_var.txt.bz2
variant pileup for sample 15 reads mapping
Paired end reads from sample 15 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample15_pileup_var.txt.bz2
variant pileup for sample 16 reads mapping
Paired end reads from sample 16 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
sample16_pileup_var.txt.bz2
arabis alpina filtered snp table
A summary of the filtered 127041 SNPs.The file provide : the contig name, the position on the contig, the reference base, the variant base, the global coverage, the average coverage, the phred mapping quality
snp_table.txt.bz2