Phylogenetic and comparative genomics establishes origin of paralogy between homologs of AtMYB42 and AtMYB85 in last common ancestor of Brassicaceae via segmental duplication

Abstract

Origin and evolution of secondary cell wall is considered key to colonization of terrestrial habitat by plants. The primary component of secondary cell wall, lignin, imparts strength and rigidity and enables plants to endure negative pressure created during transpiration. Members of the MYB transcription family, AtMYB42 and AtMYB85, play critical roles as regulators of lignin biosynthesis. Inspite of their functional significance, evolutionary history of homologs of AtMYB42 and AtMYB85 across land plants remains to be investigated. Our analysis revealed that homologs of AtMYB42 and AtMYB85 as two distinct genes are not present in any plant lineage outside Brassicaceae and only the ancestral form exists as AtMYB42/AtMYB85. Analysis of homologs of AtMYB42 and AtMYB85 across green plants combined with comparative genomics, selection pressure, and character-state reconstruction reveals that AtMYB42 and AtMYB85 are paralogous, and arose via segmental duplication, which may coincide with the α-event of WGD that occurred after the split of Brassicaceae-Caricaceae from the last common ancestor. Within Brassicaceae, homeologs and paralogs that arose as a result of polyploidization, and species- and lineage-specific changes could be observed. For instance, homologs of AtMYB42 were found to be deleted from the entire Brassica lineage. Analysis of homeologous segments in neopolyploids (B. napus, B. juncea, Camelina sativa), and meso-polyploid (B. rapa) revealed differential degrees of gene loss and retention. In Brassicaceae, homologs of AtMYB42 were found to be under purifying selection and of AtMYB85 under positive selection. High sequence identity in the coding region between homologs of AtMYB42 and AtMYB85 is indicative of redundant roles, and the loss of homologs of AtMYB42 in Brassica may be compensated by presence of AtMYB85 homologs and homeologs. The study thus forms the basis to investigate questions on regulatory diversification owing to variation in cis-elements between the paralogs and among homeologs, and, impact of differential selection pressure vis-a-vis redundant function.