Genome structure evolution in Brassica: insight from pericentromeric regions
The pericentromeric regions of plant genomes are among the most rapidly evolving genomic parts, which are found to be largely driven by some major mechanisms such as LTR-retrotransposons proliferation, gene conversions, and segmental duplications(Liao et al., 2018). Comparison of the pericentromeric regions among three assemblies of the B. rapa with different assembly quality (Supplementary Fig. 1E) revealed that the current assembly resolved a larger part of pericentromeric repetitive regions than other two assemblies (Supplementary Fig. 1A,B,C,D). A large part of the pericentromeric regions was missed in the other two assemblies, especially theB. rapa var. pekinensis assembly. This result shows that high contiguous genome assemblies are required for comparative genomic analysis of highly repetitive regions.
Thus, for interspecies comparison, we selected highly contiguous assemblies for two closely related Brassica species, B. nigra and B. oleracea , which represent two other Brassicagenome types (BB and CC), and compared the genome structure and sequence features at the pericentromeric regions of all chromosomes among these three Brassica species or genome types. We found that the pericentromeric regions of chromosome 5 and 6 in B. rapaexperienced a lineage-specific LTR-retrotransposon amplification history. For example, comparison of chromosome 5 between B. rapaand B. nigra (Fig. 6A) showed that B. rapa has a clear enrichment of LTR retrotransposon compared to the orthologous pericentromeric regions of B. nigra although the syntenic relationship of the whole chromosome is well retained between these two species. This difference is more likely to be caused by lineage specific LTR retrotransposon amplification history since their divergence. While comparison between B. rapa and B. oleracea (Fig. 6B) showed that the synteny of chromosome 5 breaks at the centromere region (see also Fig. 5B) and the break event is more likely to occur in theB. oleracea lineage since the B. rapa share the synteny block with B. nigra (Fig. 6A), while the B. oleracea does not (Fig, 6C). Thus, chromosome rearrangements may be an alternative cause for the different genome structure features observed in the pericentromeric regions. Similarly, the comparison of chromosome 6 revealed an analogous pattern (Fig. 6D,E,F).