Dataset Information

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

ABSTRACT: Long 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.In 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.We 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.

SUBMITTER: Deng F

PROVIDER: S-EPMC5785843 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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

Deng Fenni F Zhang Xiaopei X Wang Wei W Yuan Rui R Shen Fafu F

BMC plant biology 20180125 1

<h4>Background</h4>Long 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 e ...[more]

PMID: 29370759

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Project description:Melatonin (MT; N-acetyI-5-methoxytryptamine) is an amine hormone involved in abiotic stress resistance. Previous studies have confirmed that melatonin can promote seed germination, mediate physiological regulation mechanisms, and stimulate crop growth under stress. However, the osmotic regulation mechanism by which exogenous melatonin mediates salt tolerance in cotton is still largely unknown. To investigate the effect of salt stress on melatonin concentration in germinating cotton seeds, we analyzed melatonin content over time during seed germination under different treatments. Melatonin content reached its minimum at day 6, while cotton germination rates peaked at day 6, indicating melatonin content and seed germination are correlated. Then we investigated the effects of 10-100 μM melatonin treatments on membrane lipid peroxides and osmotic adjustment substances during cotton seed germination under salt stress. Salt stress led to electrolyte leakage (EL) as well as accumulations of hydrogen peroxide (H2O2), malondialdehyde (MDA), organic osmotic substances (i.e., proline, soluble sugars), and inorganic osmotic substances (i.e., Na+, Cl-). Meanwhile, the contents of melatonin, soluble proteins, and K+ as well as the K+/Na+ balance decreased, indicating that salt stress inhibited melatonin synthesis and damaged cellular membranes, seriously affecting seed germination. However, melatonin pretreatment at different concentrations alleviated the adverse effects of salt stress on cotton seeds and reduced EL as well as the contents of H2O2, MDA, Na+, and Cl-. The exogenous application of melatonin also promoted melatonin, soluble sugar, soluble proteins, proline, and K+/Na+ contents under salt stress. These results demonstrate that supplemental melatonin can effectively ameliorate the repression of cotton seed germination by enhancing osmotic regulating substances and adjusting ion homeostasis under salt stress. Thus, melatonin may potentially be used to protect cotton seeds from salt stress, with the 20 μM melatonin treatment most effectively promoting cotton seed germination and improving salt stress tolerance.

Project description:BackgroundCotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG).ResultsAntioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as "response to oxidative stress", "response to salt stress", "response to water deprivation", "cation transport", "metal ion transport", "superoxide dismutase", and "reductase". Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton.ConclusionCollectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.

Dataset Information

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

Publications

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

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