Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication.

Chinese cabbage (Brassica rapa subsp. pekinensis) is an economically important vegetable that has encountered four rounds of polyploidization. The fourth event, whole genome triplication (WGT), occurred after its divergence from Arabidopsis. Expansins (EXPs) are cell wall loosening proteins that participate in cell wall modification processes. In this study, the impacts of WGT on the B. rapa expansin (BrEXP) superfamily were evaluated. Whole genome screening of B. rapa identified 32 loci coding 53 expansin genes. Fifteen of the loci maintained a single gene copy, 15 maintained two gene copies and 2 maintained three gene copies. Six loci had no synteny to any Arabidopsis thaliana orthologs. Two loci were involved in tandem duplication. Segmental duplication and fragment recombination were dominant in accelerating BrEXP evolution. Three genes (BrEXPA7, BrEXLA1 and BrEXLA2) lost one of their ancestral introns, two genes (BrEXPA18 and BrEXPB6) gained new introns, and a domain tandem repeat (BrEXPA18) and domain recombination (Bra016981; not considered as expansin) were observed in one gene each. Further, domain deletion was observed in an additional five genes (Bra033068, Bra000142, Bra025800, Bra016473 and Bra004891, not considered as expansins) that lost one of their expansin-specific domains evolutionarily. These findings provide a basis for the evolution and modification of the BrEXP superfamily after a WGT event, which will help in determining the functional characteristics of BrEXPs.