Gene loss/retention and evolutionary pattern of ascorbic acid biosynthesis and recycling genes in Brassica rapa following whole genome triplication

Abstract

Ascorbic acid (AsA) is an inevitable antioxidant found abundantly in higher plants. Despite the importance of AsA in plants, how AsA biosynthesis (ABGs; d-mannose/l-galactose pathway) and AsA recycling genes (ARGs) evolved through polyploidization has not been addressed to date. Here, we evaluated the impacts of whole genome triplication (WGT) on ABGs and ARGs in Chinese cabbage (Brassica rapa ssp. pekinensis), which diverged from Arabidopsis thaliana before the WGT event. Twenty-three ABGs coded in 13 loci representing nine different enzyme classes and 29 ARGs coded in 19 loci representing five different enzyme classes were identified in the B. rapa genome by whole-genome screening through comparative genomic analyses. Five of these loci maintained three gene copies, 10 loci maintained two gene copies and the majority of the loci (n = 17) maintained single gene copies. Segmental (62 %) and tandem duplication (6 %), and fragment (21 %) and large-scale recombination (10 %) events accelerated the diversification of ABGs and ARGs. Thirteen of the 52 (25 %) identified genes experienced intron losses and two (4 %) experienced intron gains implying that intron losses outnumbered intron gains. The expansion and the retention of ABGs and ARGs were similar to the whole genome gene expansion and retention (P > 0.05). These findings provide new insights into the structural characteristics and evolutionary trends of ABGs and ARGs. In addition, our data could become a useful resource to further the functional characterization of these genes.