Molecular Evolution of RAMOSA1 (RA1) in Land Plants

Abstract

RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controlsplant meristem fate and identity and has played an important role in maize domestication. Despiteits importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood.In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequencelineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions.Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditionalnuclear localization signal. Here, we report that copies diversified their coding region and, with it,their protein structure, suggesting different patterns of DNA binding and protein–protein interaction.In addition, each of the retained copies diversified regulatory elements along their promoter regions,indicating differences in their upstream regulation. Taken together, the evidence indicates that theRA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalizationenabled by gene duplication.