Asymmetrical Genome Evolution and its Impact on Trait Formation in Brassica Crops.

Genome polyploidization has provided significant sources of genetic variation for plant adaptive evolution and new species formation. However, the way in which molecular evolution of polyploid genomes builds up genetic architecture underlying speciation is unclear and its impact imposed on trait formation which comes from synergistic duplicate genes of polyploidy genomes is unknown. Brassica is an ideal model to address these questions. Here, we used Arabidopsis thaliana as an outgroup to conduct comparative genome analysis of newly sequenced Brassica oleracea, B. rapa and B. napus.

We revealed multi-layered modes of asymmetrical interspecific and intraspecific genome evolution. Between parallel species B. oleracea and B. rapa, these layers of asymmetry include: gene retention rates, TE amplification, gene tandem duplication and alternative splicing variants between the two sister species; Asymmetry between subgenomes within species: subgenomic gene loss, great variations between paralogs at the DNA sequence level, expression differentiation of triplicated, α-duplicated and tandem duplicated genes across different tissues in the two diploid species, DNA sequence variation (Liu et al. Nature Communications 5:3930, 2014) and homeologous exchanges (Chalhoub et al. Science, 2014), epigenomes and recombination between the genomes A and C in B. napus. The epigenomes include small RNA, DNA methylation and histone modification. Further, we used GWAS associated markers from a large population to have revealed differences in detectable traits such as flowering time and oil content between syntenic regions of subgenomes A and C. These patterns provide new insight into genome evolution underlying speciation and trait formation.