Genome-wide characterization of microRNA in foxtail millet (Setaria italica)

Fei Yi,Yuwei Liu,Xin Qi,Shaojun Xie,Jingjuan Yu

doi:10.1186/1471-2229-13-212

Abstract

BackgroundMicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood.ResultsIn this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing.ConclusionsWe predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.

Highlights

MicroRNAs are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants
Three small RNAs (smRNAs) datasets of foxtail millet were downloaded from the Comparative Sequencing of Plant Small RNAs web site [29]
Only 65% and 82% singletons were found in Arabidopsis [8] and rice [22], respectively, suggesting that the smRNAs in foxtail millet are as complex as they are in rice, and more complex than in Arabidopsis

Summary

Introduction

MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. MicroRNAs (miRNAs) are 20 ~ 22 nucleotide (nt) noncoding small RNAs (smRNAs). Most primary miRNAs (pri-miRNAs) are transcribed from miRNA genes by RNA polymerase II (RNApol II), while others are transcribed by RNA polymerase III (RNApol III) [1]. The nascent pri-miRNA transcripts are first processed into 60 to 500 nt pre-miRNAs by DICER-LIKE1 (DCL1) [2]. The pre-miRNAs undergo a second cleavage in the nucleus, releasing an RNA duplex containing the mature miRNA and the miRNA* sequences. The mature miRNA is incorporated into an RNA-induced silencing complex (RISC) that contains

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