Tandemly duplicatedMYBgenes specifically in the Phaseoleae lineage are functionally diverged in the regulation of anthocyanin biosynthesis

Abstract

AbstractGene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean genome is characterized by a large extent of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that tandem duplication ofMYBgenes, which occurred specifically in the Phaseoleae lineage, exhibited a stronger purifying selection in soybean compared to common bean. To gain insights into the diverse functions of theseMYBgenes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, metabolite, and evolutionary history of fourMYBgenes (GmMYBA5,GmMYBA2, GmMYBA1andGlyma.09g235000), which were presumably generated by tandem duplication in soybean. Our data revealed thatGlyma.09g235000had become a pseudogene, while the remaining threeMYBgenes exhibited strong transcriptional activation activity and promoted anthocyanin biosynthesis in different soybean tissues. Furthermore,GmMYBA5produced distinct compounds inNicotiana benthamianaleaves compared toGmMYBA2andGmMYBA1due to variations in their DNA binding domains. The lower expression of anthocyanin related genes inGmMYBA5resulted in lower levels of anthocyanins compared toGmMYBA2andGmMYBA1. Metabolomics analysis further demonstrated the diverse and differential downstream metabolites, suggesting their functional divergence in metabolites following gene duplication. Together, our data provided evidence of functional divergence within theMYBgene cluster following tandem duplication, which shed light on the potential evolutionary direction of gene duplications during legume evolution.