Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

Abstract

BackgroundMicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research.ResultsIn our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (AtSGS3) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.ConclusionsWe have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

“…PARE data of Arabidopsis seedlings and inflorescences were generated by this study and PARE data of rice inflorescences and soybean seeds were published by Zhou et al (2010) and Song et al (2011). Blue bars indicate positions falling in the translational frame (frame 1) of annotated CDS if 59-truncated ends represent the 59 edge of a ribosome and the distance from the 59 edge of a ribosome to the first base of the A site is 17 nucleotides.…”

“…The soybean PARE data plotted were retrieved from the data set published by Song et al (2011). In Frerigmann and Gigolashvili, 2014).…”

Genome‐wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

“…High‐throughput next‐generation sequencing (NGS) emerged as a powerful tool to identify miRNAs from animals and plants (Calla & Geib, 2015; Guillem, Bastian, Maria‐Dolors, & Xavier, 2016; Nandety, Sharif, Kamita, Ramasamy, & Falk, 2015; Song et al., 2011; Wang et al., 2012; Wu et al., 2013). It has accelerated the pace of miRNA discovery from various animals and plants (Avesson, Reimegard, Wagner, & Söderbom, 2012; Burnside et al., 2008; Ge et al., 2013; Hu et al., 2012; Kang et al., 2012; Koh et al., 2010; Zhang et al., 2012).…”

Analysis of promoters of microRNAs from a Glycine max degradome library

“…Soybean was the first legume species with a published high-quality draft genome sequence (Schmutz et al, 2010). Because miRNAs play an important regulatory role in a wide variety of developmental and metabolic processes in plants, more and more soybean miRNAs have been identified (Zhang et al, 2008;Chen et al, 2009;Wang et al, 2009;Guo et al, 2011;Kulcheski et al, 2011;Li et al, 2011;Song et al, 2011;Wong et al, 2011;Zeng et al, 2012;Hu et al, 2013), but the features of the upstream sequences of these miRNAs have not been comprehensively analyzed. Core promoters and cis-acting elements of 82 soybean miRNAs from the miRBase database were analyzed by bioinformatics methods (Liu et al, 2010), but this analysis involved a relatively small number of miRNA genes.…”