Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing.

Min Liu,Min-Gui Zhao,Rujin Chen,Wen-Hao Zhang,Tian-Zuo Wang

doi:10.1186/s12870-015-0530-5

Min Liu, Min-Gui Zhao + Show 3 more

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https://doi.org/10.1186/s12870-015-0530-5

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Abstract

BackgroundLong non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. However, information regarding the number, sequences, characteristics and potential functions of lncRNAs in plants is so far overly limited.ResultsUsing high-throughput sequencing and bioinformatics analysis, we identified a total of 23,324 putative lncRNAs from control, osmotic stress- and salt stress-treated leaf and root samples of Medicago truncatula, a model legume species. Out of these lncRNAs, 7,863 and 5,561 lncRNAs were identified from osmotic stress-treated leaf and root samples, respectively. While, 7,361 and 7,874 lncRNAs were identified from salt stress-treated leaf and root samples, respectively. To reveal their potential functions, we analyzed Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.ConclusionsLncRNAs are likely involved in regulating plant’s responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes. These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0530-5) contains supplementary material, which is available to authorized users.

Highlights

Long non-coding RNAs have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms
High-throughput sequencing Six cDNA libraries were constructed using mRNA isolated from leaves and roots of M. truncatula seedlings treated with osmotic stress (OS), salt stress (SS), and control (CK) and complementary sequences of synthetic adaptors
In this study, we identified 23,324 putative Long non-coding RNAs (lncRNAs) from six RNA-seq libraries of M. truncatula by highthroughput sequencing, of which 11,641 and 13,087 lncRNAs are found to be responsive to osmotic stress and salt stress, respectively

Summary

Introduction

Long non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. Non-coding RNAs (ncRNAs) are a set of RNAs that have no capacity to code for proteins. They are used to be considered as inconsequential transcriptional “noises”, because of limited information for their functions [1, 2]. LncRNAs are defined as a group of ncRNAs that have a length of more than 200 nucleotides [6] They are usually expressed at low levels and lacking sequence similarities among species, exhibit tissue and cell-specific expression patterns, and transcripts are localized to subcellular compartments [4, 7]. In Arabidopsis thaliana, >30 % of lncRNAs are intergenic, and antisense lncRNAs are abundant [9, 10]

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