Abstract
The R2R3-MYB transcription factors play critical roles in various processes in embryophytes (land plants). Here, we identified genes encoding R2R3-MYB proteins from rhodophytes, glaucophytes, Chromista, chlorophytes, charophytes, and embryophytes. We classified the R2R3-MYB genes into three subgroups (I, II, and III) based on their evolutionary history and gene structure. The subgroup I is the most ancient group that includes members from all plant lineages. The subgroup II was formed before the divergence of charophytes and embryophytes. The subgroup III genes form a monophyletic group and only comprise members from land plants with conserved exon–intron structure. Each subgroup was further divided into multiple clades. The subgroup I can be divided into I-A, I-B, I-C, and I-D. The I-A, I-B, and I-C are the most basal clades that have originated before the divergence of Archaeplastida. The I-D with the II and III subgroups form a monophyletic group, containing only green plants. The II and III subgroups form another monophyletic group with Streptophyta only. Once on land, the subgroup III genes have experienced two rounds of major expansions. The first round occurred before the origin of land plants, and the second round occurred after the divergence of land plants. Due to significant gene expansion, the subgroup III genes have become the predominant group of R2R3-MYBs in land plants. The highly unbalanced pattern of birth and death evolution of R2R3-MYB genes indicates their important roles in the successful adaptation and massive radiation of land plants to occupy a multitude of terrestrial environments.
Highlights
It is widely accepted that transcription factors (TFs) play vital roles in all aspects of plant life (Riechmann and Ratcliffe, 2000; Singh et al, 2002)
We identified R2R3-MYB homologous genes from transcriptomic data of 191 species from charophyte, chlorophyte, glaucophyte, Chromista, rhodophyte, and liverworts, which were obtained from the 1KP project5
Unlike traditional gene subgroup classification, we classified R2R3-MYB genes mainly based proteins in land plants were found in the subgroups III
Summary
It is widely accepted that transcription factors (TFs) play vital roles in all aspects of plant life (Riechmann and Ratcliffe, 2000; Singh et al, 2002). 5% of protein-coding genes (∼1500) in the Arabidopsis genome encode transcription factors (Riechmann et al, 2000), Origins and Expansion of R2R3-MYB Transcription Factors. The availability of these new genomic and transcriptomic data makes it possible to conduct a more comprehensive phylogenetic inference of the. We classified R2R3-MYB genes into three subgroups (I, II, and III), representing their evolutionary origins. Our further interrogation of the evolutionary history of each subgroup revealed two major expansion events during the evolution of subgroup III. We speculated these expansion events might have contributed to the successful adaptation of land plants to terrestrial environments
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