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Asymmetry of evolution and selection response of subgenomes 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 whether there are any differences in polyploidsubgenomes’s responses to selection 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. rapaand B. napus. We revealed multi-layered modes of asymmetrical interspecific and intraspecific genome evolution. Between parallel species B. oleracea and B. rapa, these layers include: asymmetrical gene retention rates,asymmetrical TE amplification, asymmetrical tandem duplication of genes and asymmetrically alternative splicing variantsbetween the two sister species; Between subgenomes within species, these layers include: massive and asymmetrical 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, asymmetrical recombination on A and C in B. napus. In addition, the predominant mechanism for gene loss is small deletion, rather than asymmetrical cross-over. These patterns provide new insight into genome evolution underlying speciation and trait formation and will underpin research into genetic improvement of these important crops
