R2R3-MYBGene Evolution in Plants, Incorporating Ferns into the Story

Abstract

Premise of research. MYB transcription factors are one of the largest families of genes in land plants. They are involved in many regulatory processes, such as primary and secondary metabolism, cell fate and identity, developmental processes, and responses to biotic and abiotic stresses. Phylogenetic studies have mainly focused on R2R3-MYB evolution in seed plants; however, a comprehensive sampling across land plants is lacking, as none have included ferns. Methodology. To better understand the evolution of R2R3-MYB genes in land plants, we surveyed the R2R3-MYB gene sequences from six genomes belonging to the main lineages of land plants (bryophytes, lycophytes, ferns, angiosperms, and gymnosperms). In addition, we searched transcriptome sequences of selected fern and lycophyte transcriptomes. We assembled a nucleotide matrix of the MYB domain and conducted maximum likelihood analyses to infer phylogenetic relationships and gene-tree reconciliation analyses to infer gene duplications. We labeled the main clades with the known MYB functions onto the resulting tree. To detect reported as well as new conserved motifs, we ran protein motif analyses through MEME. Pivotal results. Our results support previous studies indicating that R2R3-MYBs in seed plants are more diverse than in any other lineage of vascular plants. Most of the well-supported clades recovered are inferred to be already present in the ancestor of land plants. We found that ferns have numerous copies of R2R3-MYBs, although not as many as seed plants. Protein motif analyses revealed that R2R3-MYB motifs are highly conserved across land plants, suggesting that most R2R3-MYB orthologues, including those of ferns, might have DNA-binding capabilities and could be involved in regulatory processes that are similar to those of their angiosperm homologues. Our analyses showed that there are no fern orthologues of the angiosperm MYB leaf developmental genes ARP, raising interesting questions about the evolution and origin of leaves in ferns and seed plants. Conclusions. Our results provide the phylogenetic context for research on the genetic and functional evolution of an important gene family of developmental and metabolic regulators across the plant tree of life.