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.

BackgroundSuperoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton.ResultsIn the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified and phylogenetically classified into five subgroups which corroborated their classifications based on gene-structure patterns and subcellular localizations. The GhSOD sequences were distributed at different densities across 12 of the 26 chromosomes. The conserved domains, gene family evolution cis-acting elements of promoter regions and miRNA-mediated posttranscriptional regulation were predicted and analyzed. In addition, the expression pattern of 18 GhSOD genes were tested in different tissues/organs and developmental stages, and different abiotic stresses and abscisic acid, which indicated that the SOD gene family possessed temporal and spatial specificity expression specificity and may play important roles in reactive oxygen species scavenging caused by various stresses in upland cotton.ConclusionsThis study describes the first genome-wide analysis of the upland cotton SOD gene family, and the results will help establish a foundation for the further cloning and functional verification of the GhSOD gene family during stress responses, leading to crop improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3768-5) contains supplementary material, which is available to authorized users.

Superoxide dismutases (SODs) are key enzymes functioning as the first line of antioxidant defense by virtue of the ability to convert highly reactive superoxide radicals to hydrogen peroxide and molecular oxygen. SOD plays a central role in protecting plants against the toxic effects of reactive oxygen species generated during normal cellular metabolic activity or as a result of various environmental stresses. Our review focuses on the characteristics of expression of SOD genes, the mechanisms regulating expression of SOD genes at transcriptional, posttranscriptional, and translation levels, and their functional role(s) during development and in response to biotic or abiotic stresses. We propose two important research directions: studying SOD at the genome-wide or proteome-wide level, and improving plant stress tolerances by selecting varieties using transgenic technology.

BackgroundLong non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973.ResultsIn this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress.ConclusionsLncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.

The data presented in this paper is supporting the research article “Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum” [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), “Bayesian phylogenetic inference under mixed models” [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, “SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.” [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, “Pfam: the protein families database” [4].