We present here the analysis of the diploid genome sequence of
Arabis alpina a close relative of
Arabidopsis thaliana belonging to the family
Brassicaceae.
A. alpina is an emerging model organism, because of its perennial life cycle. Since it is self-compatible and genetically transformable, mutagenized populations and inbred homozygous lines can be produced.
A. alpina belongs to the tribe
Arabideae, in which several perennial and annual species can be found. The reference accession of
A. alpina Pajares was collected in the Cordillera Cantábrica mountain system in Spain and was afterwards self-fertilized for several generations by single-seed descent. Its haploid genome consists of eight chromosomes and was sequenced following a hybrid approach using 454 shotgun and 454 and Illumina paired-end sequencing with 12 kb, 3 kb and 500 bp insert size libraries. In addition, we generated 21 Mb of Sanger sequenced BAC ends for establishing long-range connections between assembled contigs. The genome size estimated by flow cytometry was 375 Mb. Subsequent hierarchical scaffolding established 38,819 scaffolds with an N50 and L50 of 788 and 166 kb, respectively. In total, this assembly contained 309 Mb of sequence (273 Mb unambiguous) covering ~82% of the expected genome size. Among the scaffolds with multiple genes, we found extensive synteny between the orthologs of
A. alpina and
A. thaliana. Comparative chromosome painting (CCP) revealed conserved order of large genomic regions with
A. thaliana enabling an additional, synteny-based scaffolding into eight pseudo-molecules representing the eight chromosomes of
A. alpina. The final assembly consists of 234 Mb (including 88% of the genes) assembled into eight pseudo-molecules and 36,267 unassigned scaffolds with a combined length of 75 Mb.
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