Sequence conservation and divergence in miR164C1 and its target, CUC1, in Brassica species

Abstract

An emerging aspect of plant development and adaptation studies is microRNA (miRNA)-mediated gene regulation and to understand post-transcriptional gene silencing (PTGS) dynamics. Studies performed within an evolutionary context, such as specific plant lineages and genome status (e.g. ploidy level) can highlight the selection pressure and constraints guiding the evolutionary trajectory of regulatory modules. We have investigated conservation and allelic diversity in one such module composed of CUC1 (CUP-SHAPED COTYLEDON 1), a NAC domain family member, and miR164C, within Brassica species. Ancestral CUC1 sequences, including those belonging to Amborellales, Nymphaeales and Austrobaileyales, harbour miR164 binding sites, implying an ancient nature of this regulatory module. We found that sequence and length polymorphisms occurred in the miR164C precursor of diploid and amphidiploid Brassica species, although the 21-nt mature sequence was invariant. In contrast, the target sequence in CUC1 exhibited polymorphism at the “seed” and “cleavage” site, otherwise governed by stringent rules of pairing for successful PTGS, implying a “relaxed” selection pressure on CUC1. Further studies are needed to improve our understanding of the functional implications of the polymorphism and single nucleotide polymorphisms that constitute allelic variation at the region responsible for PTGS within Brassica species, in context of ploidy level, and to unravel the evolutionary dynamics of the miR164C–CUC1 regulatory module within the plant kingdom.