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).