Abstract
The release of the Brassica oleracea draft genome sequence opens numerous opportunities to understand its genome structure and evolution. A 515-Mb (82% of the total genome) high-quality draft assembly was made up of 56% repetitive elements (REs). Although the contribution of REs to genome structures, organization and evolution is relatively poorly understood, advances in bioinformatics have enabled genome-wide quantification and downstream analyses of REs in plant genomes. This chapter provides an overview of the classification, abundance, and genomic organization of the major types of REs that make up the main repeat component in the B. oleracea genome. Eight elements namely, 5S and 45S nrDNA, centromeric and subtelomeric tandem repeats (CentBo1, CentBo2, BoSTRa/b, and BoSTRc), a centromeric retrotransposon (BoCRB), and a Ty1/copia LTR retrotransposon (BoCopia-1) were classified into this repeat component. Whole-genome shotgun (WGS) mapping and molecular cytogenetic analyses provided an in-depth view of the abundance and distribution of these repeats both in the in silico generated draft assembly and mitotic metaphase chromosomes. The information not only validates the abundance of repeat elements in draft genomes, but also provide an avenue for understanding overall genome structure.
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