Genomic survey of the hidden components of the B. rapa genome

The sequencing of the Brassica rapa genome has enabled better understanding of its structure and evolution, and created numerous opportunities for exploration of genome function and breeding applications. Nevertheless, the currently available completed genome sequences are estimated to cover only about 60 % of the genome, while the remaining 40 % is unassembled mainly due to the highly repetitive nature of this portion of the genome. Elucidation of the nature and distribution of repeat elements in the context of the entire genome would enhance our understanding of their role in genome structure, function, and evolution. In this chapter, we review the genomic distribution, characterization and evolutionary implications of currently identified repeat elements comprising the 'hidden' portion of the B. rapa genome. Low-coverage whole-genome sequence (WGS) was used to survey the major genomic repeats and their proportion in the B. rapa genome. Coupling this with molecular cytogenetics, we characterized the abundance and genomic distribution of seven major repeats, namely centromeric tandem repeats 1 and 2, centromeric retrotransposons, pericentromeric retrotransposons, 5S rDNA, 45S rDNA, and subtelomeric tandem repeats. These repeats accounted for approximately 20 % of the B. rapa genome, which is much more than the < 1 % covered by repeats in the currently available genome assembly. We also compared their distributions among different B. rapa accessions and in the close relative Brassica oleracea, for better understanding of the plasticity of the Brassica genomes.