Quantity, Distribution, and Evolution of Major Repeats in Brassica napus

Abstract

Repetitive elements (REs) play major roles in genome organization, size, and evolution, but are often underrepresented in genome assemblies. The recent genome assembly of the allotetraploid Brassica napus genome revealed that 48% of the genome comprised REs, including transposons and tandem repeats. In the present work, we show the overall quantity and comparative analyses of major repeat families in both the assembled and unassembled portions of the reference B. napus genome. We surveyed the abundance, distribution, diversity, and dynamics of ten major REs in the B. napus genome, which represented less than 1% of the total 1130 Mb B. napus genome in the current assembly. However, in silico mapping of raw whole-genome sequence reads from nine B. napus accessions revealed about 11% of the genome as represented by these ten repeat families. Comparative analyses of these major repeats showed their evolutionary dynamics in the B. rapa (Ar), B. oleracea (Co), and B. napus (AnCn) genomes as well as a considerable inter- and intraspecies repeat diversity among different B. napus accessions. Cytogenetic mapping of these major repeats showed their genomic abundance and distribution, with some families having a conserved subgenomic distribution pattern in the B. napus genome. Finally, the impact of genetic changes to REs and their corresponding epigenetic readjustments during B. napus evolution are also discussed in this chapter.