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Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of  Brassica rapa  (A genome),  B .  oleracea  (C) and  B .  napus  (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the  B .  rapa  and  B .  oleracea  genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our  insilico  analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three  Brassica  species. Overall, our work elucidates hidden portions of three  Brassica  genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.

Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution