Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera

Zhao-Xia Chang,Dong-Yang Guo,Ibukun A Akinyemi,Qingfa Wu

doi:10.1371/journal.pone.0204517

Abstract

MicroRNAs (miRNAs) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that act as functional regulators of post-transcriptional repression of messenger RNA. We report the identification and characterization of a conserved miRNA and 171 novel miRNAs in the migratory rice pest Sogatella furcifera by deep sequencing, which were observed to be biased towards female adults of the insect, modulating the functionality and targets of the miRNAs in sex differentiation. A switch in arm usage was also observed in 9 miRNA when compared to the insect ancestor during insect evolution. The miRNA loci showed high 5’ fidelity in both miRNA and star species and about 93.4% of WBPH miRNAs conserved within non-planthopper species were homologous with planthopper species. The novel miRNAs identified in this study provide a better understanding of the sRNA and the regulatory role of miRNA in sexual dimorphism and alteration in the expression or function of miRNAs in the rice pest.

Highlights

IntroductionAmong RNA types, microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-associated RNAs (piRNAs) are the best understood small RNAs (sRNAs) in the canonical RNAi pathway
Among RNA types, microRNAs, small interfering RNAs and Piwi-associated RNAs are the best understood small RNAs in the canonical RNAi pathway
Reads mapping to snRNAs, snoRNAs, rRNAs, tRNAs, and known miRNAs were removed from the total reads, and the remaining unannotated reads were mapped against the white-backed planthopper (WBPH) genome to predict novel miRNAs in WBPH adults using mireap software

Summary

Introduction

Among RNA types, microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-associated RNAs (piRNAs) are the best understood small RNAs (sRNAs) in the canonical RNAi pathway. Different classes of sRNA are defined by their sizes and interactions with the Argonaute (AGO) protein. 21-24 nucleotide (nt) long miRNAs involved in post-transcriptional gene expression are generated by Dcr-1 and interact with AGO1 to form a RISC complex; the miRNA guides the RISC on its gene targets by sequence-specific base-paring to repress protein translation or destabilize mRNA transcripts [1,2,3]. MiRNAs have been reported to be involved in regulating cell death and proliferation, fat metabolism and the differentiation of hematopoietic families in animal; they regulate thousands of target genes in a complex network in humans [4]. Knowledge of gene regulation via miRNAs had increased in recent years, there is still a limited understanding of the dynamic interactions between miRNAs and their targets beyond the down- and up-regulation of transcript levels of their targets binding with various genic sites [5, 6].

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