Boechera retrofracta isolate:PC18 Genome sequencing and assembly. Boechera retrofracta isolate:PC18

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions within the species. Boechera retrofracta is a diploid, sexually reproducing species and is supposed to be an ancestral parent of the apomictic species Boechera divaricarpa. De novo assembly of the B. retrofracta genome was performed using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. Initial contigs were constructed from filtered LIB400 reads by DISCOVAR. Then, the obtained contigs were extended using a BAC end sequencing (BES) library and the SSPACE scaffolder. Next, the extended contigs were scaffolded by SSPACE in two stages: at the first stage, all four MP libraries were used to produce raw scaffolds, at the second stage, raw scaffolds were linked to the intermediate scaffolds using the BES library only. Gap closing in the intermediate scaffolds was performed using GapCloser. Finally, all scaffolds with a length of less than 250 bp (i.e. less than read length of the library used for initial contig construction) were filtered out, as the corresponding short fragments most likely are assembly artefacts.