Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress

Abstract

BackgroundLong non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation.ResultsIn this study, in order to develop a comprehensive catalogue of lncRNAs in upland cotton under salt stress, we performed whole-transcriptome strand-specific RNA sequencing for three-leaf stage cotton seedlings treated with salt stress (S_NaCl) and controls (S_CK). In total we identified 1117 unique lncRNAs in this study and 44 differentially expressed RNAs were identified as potential non-coding RNAs. For the differentially expressed lncRNAs that were identified as intergenic lncRNAs (lincRNA), we analysed the gene ontology enrichment of cis targets and found that cis target protein-coding genes were mainly enriched in stress-related categories. Real-time quantitative PCR confirmed that all selected lincRNAs responsive to salt stress. We found lnc_388 was likely as regulator of Gh_A09G1182. And lnc_883 may participate in regulating tolerance to salt stress by modulating the expression of Gh_D03G0339 MS_channel. We then predicted the target mimics for miRNA in Gossypium. six miRNAs were identified, and the result of RT-qPCR with lncRNA and miRNA suggested that lnc_973 and lnc_253 may regulate the expression of ghr-miR399 and ghr-156e as a target mimic under salt stress.ConclusionsWe identified 44 lincRNAs that were differentially expressed under salt stress. These lincRNAs may target protein-coding genes via cis-acting regulation. We also discovered that specifically-expressed lincRNAs under salt stress may act as endogenous target mimics for conserved miRNAs. These findings extend the current view on lincRNAs as ubiquitous regulators under stress stress.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1238-0) contains supplementary material, which is available to authorized users.

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

“…In the present work, a total of 2815 lncRNAs (including 566 anti-sense lncRNAs and 2249 intergenic lncRNAs) were systematically identified in duckweed under salinity condition using ssRNA-seq technology. The number of lncRNAs was about 2.5-fold higher than that reported in cotton [12], but much less than that identified in M. truncatula, maize, and wheat [13][14][15]. These results, to a certain extent, reflected the influences of sequencing depth, plant species, and applied parameters on lncRNAs discovery.…”

“…LncRNA has been illustrated to play an important regulatory role in salt stress response of many species, including cotton [12], maize [13], M. truncatula [14], and wheat [15]. However, the roles of lncRNAs have so far not been reported in duckweed upon salt treatment, which greatly inhibited the vegetative growth of duckweed [23].…”

“…With the high-speed development of next-generation sequencing, hundreds of lncRNAs have been associated with salt stress in plants through transcriptome reassembly. In cotton (Gossypium hirsutum), a total of 1117 unique lncRNAs were identified, and 44 were differentially expressed under salt treatment [12]. In maize (Zea mays), a total of 48,345 distinct lncRNAs were identified, of which 1710 were responsive to both salt and boron stress [13].…”

Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum

“…Previous studies proved that lncRNAs can function as ceRNAs and regulate gene expression at the post-transcriptional level He et al, 2019). Additionally, lncRNAs serve as target mimics that interact with miRNAs thereby preventing miRNAs from completely degrading their targets (Wu et al, 2013;Deng et al, 2018;Meng et al, 2018). To assess the regulatory patterns of non-coding RNA-related ceRNA interactions in sweet sorghum roots, lncRNA-miRNA-mRNA pairs were predicted in the treated and control of M-81E and Roma samples.…”

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

“…Advances in next‐generation sequencing resulted in the unearthing of lncRNAs in several plants, such as Arabidopsis thaliana , Medicago truncatula , Triticum aestivum , Cajanus cajan , cucumber, poplar, maize, rice, grapevine, mulberry, sea buckthorn, kiwifruit, and cotton . Recent studies have elucidated regulatory roles of the multitude lncRNAs present in the plant genome in diverse biological processes, such as flowering, reproduction, photo‐morphogenesis, vernalization, organ development, cell cycle, biotic and abiotic stress responses, etc.…”