Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels in a variety of ways. They play important roles in biological processes such as chromatin remodeling, transcriptional activation, transcriptional interference, RNA processing, and mRNA translation. lncRNAs have important functions in plant growth and development; biotic and abiotic stress responses; and in regulation of cell differentiation, the cell cycle, and the occurrence of many diseases in humans and animals. In this review, we summarize the functions and mechanisms of lncRNAs in plants, humans, and animals at different regulatory levels.

To fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activity. New high-throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient unbiased manner. We applied a strand-specific method to sequence bacterial transcripts using Illumina's high-throughput sequencing technology. The resulting sequences were used to construct genome-wide transcriptional profiles. Novel bioinformatics analyses were developed and used in combination with proteomics data for the qualitative classification of transcriptional activity in defined regions. As expected, most transcriptional activity was consistent with predictions from the genome annotation. Importantly, we identified and confirmed transcriptional activity in areas of the genome inconsistent with the annotation and in unannotated regions. Further analyses revealed potential RpoN-dependent promoter sequences upstream of several noncoding RNAs (ncRNAs), suggesting a role for these ncRNAs in RpoNdependent phenotypes. We were also able to validate a number of transcriptional start sites, many of which were consistent with predicted promoter motifs. Overall, our approach provides an efficient way to survey global transcriptional activity in bacteria and enables rapid discovery of specific areas in the genome that merit further investigation.

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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.

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The Menispermaceae, a largely tropical family of dioecious and predominantly climbing plants, have been the subject of various molecular studies that confirmed its monophyly and the para‐ and polyphyly of most of the currently recognized tribes. The newly recognized assemblages have been variously named informally in different studies. Here we present a comprehensive phylogenetic hypothesis of the Menispermaceae based on the analyses of three molecular markers (matK, trnL‐F, ndhF) and 41 morphological characters for the most extensive taxonomic and geographic sampling of the family as compared to earlier studies. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood, and Bayesian approaches. Our results of the combined molecular and total‐evidence datasets corroborate earlier findings, with an improved support for major clade contents. A new tribal classification of the Menispermaceae is proposed, in which nine clades are grouped within the subfamilies Chasmantheroideae and Menispermoideae, forming themselves two well‐supported clades. Within the Chasmantheroideae, the two clades recovered are here recognized as tribes Burasaieae and Coscinieae; within the Menispermoideae the seven identified clades are recognized as tribes Anomospermeae, Cissampelideae, Limacieae, Menispermeae, Pachygoneae, Spirospermeae, and Tiliacoreae. Of these, Spirospermeae is newly described, while the names, if not the circumscriptions, of the remaining tribes are adopted from earlier treatments. The subfamilies and most tribes here identified are further diagnosed by unique combinations of morphological characters. A few genera not sampled for the molecular analysis are provisionally assigned to the recognized tribes based on their floral, fruit, endocarp, and seed features.

Catalases (CATs), which were coded by the catalase gene family, were a type notably distinguished ROS-metabolizing proteins implicated to perform various physiological functions in plant growth, development and stress responses. However, no systematical study has been performed in cotton. In the present study, we identified 7 and 7 CAT genes in the genome of Gossypium hirsutum L. Additionally, G. barbadense L., respectively. The results of the phylogenetic and synteny analysis showed that the CAT genes were divided into two groups, and whole-genome duplication (WGD) or polyploidy events contributed to the expansion of the Gossypium CAT gene family. Expression patterns analysis showed that the CAT gene family possessed temporal and spatial specificity and was induced by the Verticillium dahliae infection. In addition, we predicted the putative molecular regulatory mechanisms of the CAT gene family. Based on the analysis and preliminary verification results, we hypothesized that the CAT gene family, which might be regulated by transcription factors (TFs), alternative splicing (AS) events and miRNAs at different levels, played roles in cotton development and stress tolerance through modulating the reactive oxygen species (ROS) metabolism. This is the first report on the genome-scale analysis of the cotton CAT gene family, and these data will help further study the roles of CAT genes during stress responses, leading to crop improvement.

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