Evolutionary Comparison of Two Combinatorial Regulators of SBP-Box Genes, MiR156 and MiR529, in Plants

PLoS One. 2015 Apr 24;10(4):e0124621. doi: 10.1371/journal.pone.0124621. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Conserved Sequence
  • Evolution, Molecular*
  • Gene Deletion
  • Gene Duplication
  • Gene Expression Regulation, Plant*
  • Genes, Plant*
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Nucleic Acid Conformation
  • Oryza / genetics
  • Plants / genetics*
  • RNA Precursors
  • RNA Stability
  • Sequence Analysis, DNA

Substances

  • MicroRNAs
  • RNA Precursors

Grants and funding

This work was supported by the National Natural Science Foundation of China (grant no. 31200172), Promotive Research Fund for Excellent Young and Middle-Aged Scientists of Shandong Province (BS2013SW003), Special Fund for BGI-Yunnan’s High Throughput Sequencing Platform (P.R. China, Yunnan Provincial Science and Technology Department, 2013 DA008), The Research of High Throughput Sequencing Technology in the Application of Prevention and Control of the Mediterranean Anemia High-Risk Groups (P.R. China, Yunnan Province, 2014FC003), The Cultivation of Backup Young and Middle-Aged Academic Technology Leaders in Yunnan Province (P.R. China, Yunnan Province, 2014HB053), and The Application of Genomics Technology in Notoginseng Breeding (P.R. China, Yunnan Province, 2014BC005). 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.