Abstract
A complete picture of the evolution of miRNA combinatorial regulation requires the synthesis of information on all miRNAs and their targets. MiR156 and miR529 are two combinatorial regulators of squamosa promoter binding protein-like (SBP-box) genes. Previous studies have clarified the evolutionary dynamics of their targets; however, there have been no reports on the evolutionary patterns of two miRNA regulators themselves to date. In this study, we investigated the evolutionary differences between these two miRNA families in extant land plants. Our work found that miR529 precursor, especially of its mature miRNA sequence, has a higher evolutionary rate. Such accelerating evolution of miR529 has significantly effects on its structural stability, and sequence conservation against existence of itself. By contrast, miR156 evolves more rapidly in loop region of the stable secondary structure, which may contribute to its functional diversity. Moreover, miR156 and miR529 genes have distinct rates of loss after identical duplication events. MiR529 genes have a higher average loss rate and asymmetric loss rate in duplicated gene pairs, indicating preferred miR529 gene losses become another predominant mode of inactivation, that are implicated in the contraction of this family. On the contrary, duplicated miR156 genes have a low loss rate, and could serve as another new source for functional diversity. Taken together, these results provide better insight into understanding the evolutionary divergence of miR156 and miR529 family in miRNA combinational regulation network.
Highlights
MicroRNAs are small, non-coding RNA molecules that regulate gene expression by binding to target mRNA transcripts, leading to either translational repression or mRNA degradation
It has been reported that ubiquitously expressed genes evolve more slowly than tissue-specific genes, which suggests that the extent to which genes are expressed is critical for their evolutionary rates in multicellular organisms [27]
We conjectured that narrowly expressed miR529 genes might have higher evolutionary rate than broadly expressed miR156 genes
Summary
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression by binding to target mRNA transcripts, leading to either translational repression or mRNA degradation. A growing body of evidence indicates that, in plants, a single miRNA can target and regulate multiple transcripts and the same genes can be targeted by a number of PLOS ONE | DOI:10.1371/journal.pone.0124621. Evolutionary Comparisons of MiR156 and MiR529 in Plants. BGI provided support in the form of salaries for authors L-ZL and LC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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