Genome Assembly and Annotation of Boechera holboellii (fam. Brassicaceae)

Closely related to Arabidopsis, genus Boechera is known to contain both sexual and apomictic species or forms within species. Boechera holboellii is a diploid sexual species belonging to this genus and is supposed to be one of the parental species for at least one apomictic species Boechera divaricarpa.

We performed de novo genome assembly of this species using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries and achieved N50 of scaffolds slightly greater than 1Mb. Contigs and initial scaffolds have been assembled by DISCOVAR and then final scaffolds have been generated by SSPACE and GapCloser. We also have annotated more than 25000 protein-coding genes by hybrid approach based on protein homology to proteins of the 4 closely related species and de novo prediction methods.

B.holboelli is a plant of particular interest as an ancestor of various hybrids including apomictic species. Genome assembly of hybrid species is still a problem and sequences of parental genomes will greatly help to solve this challenge. Ancestral genomes are also required for further comparative analysis and investigation of apomixis origin.