Conservation and divergence of small RNA pathways and microRNAs in land plants

Chenjiang You,Jie Cui,Lei Gao,Hong Ma,Hui Wang,Xuemei Chen,Li-Yaung Kuo,Xinping Qi,Beixin Mo

doi:10.1186/s13059-017-1291-2

Abstract

BackgroundAs key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants.ResultsUsing 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms.ConclusionsOur phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants.

Highlights

As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms
Diversification of DCL and AGO genes in land plants Previous studies showed that many genes involved in small RNA pathways are conserved in seed plants, lycophytes, and mosses [36]
In order to investigate components of the small RNA machinery in sister species of seed plants, we sequenced the transcriptomes of the hornwort F. fuciformis, four species from all three orders of lycophytes, and 21 species covering all 11 orders of ferns (Fig. 1; Additional file 1: Table S1)

Summary

Introduction

As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. Both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants. RNAs are some of the most important components of life They serve as mediators between genes and proteins as depicted in the central dogma [1], and act as direct regulators of life processes, such as in the form of ribozymes and regulatory RNAs [2, 3]. Afterwards, one strand of the duplex associates with ARGONAUTE1 (AGO1) to form the RNA-induced silencing complex (RISC) [5], which recognizes and represses target mRNAs [12, 13]

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Conclusion