The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion

Abstract

R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.

Evolutionarily Conserved Alternative Splicing Across Monocots

“…The MYB genes identified in this network belong to the R2R3-MYB family. The R2R3-MYB family has undergone expansion in plants (Du et al 2014) and plays many important plant-specific roles. Furthermore, there are many kinase and phosphatase related genes in close association with genes responsible for phosphorylation and dephosphorylation of splicing regulators, such as serine-threonine protein kinase (CIPK3), calcium-dependent protein kinase 29 (CPK29), CBL-interacting protein kinase 9 (CIPK9), and calcineurin b-like protein (CBL1).…”

Genetic analysis of the liverwort Marchantia polymorpha reveals that R2R3MYB activation of flavonoid production in response to abiotic stress is an ancient character in land plants

“…For the residues within the MYB domain identified as differing between SG6 and the other subgroups (Schwinn et al ., ), in most cases Mp MYB02 and Mp MYB14 are more closely aligned to SG5/7 and not SG6. This is supported by the phylogenetics, as no SG6 sequences have been identified from nonangiosperm species (Du et al ., ; and Fig. S1).…”

Diversification of Root Hair Development Genes in Vascular Plants

“…Thus, it is tempting to speculate that the evolution of the WER/MYB23 genes was the critical factor in the origin of the Arabidopsis type 3 pattern. However, a recent extensive analysis of MYB genes in multiple species showed that subgroup 15 includes members from several type 1 eudicots (Du et al, 2015), complicating the potential linkage between this subgroup and the type 3 pattern. Interestingly, the patterning of epidermal hairs (trichomes) on the leaf surface of Arabidopsis also relies on a member of this MYB subgroup 15, the GL1 gene (Larkin et al, 1993), implying shared evolution of these patterning mechanisms.…”