Global identification of full-length cassava lncRNAs unveils the role of CRIR1 in cold stress response

Long non-coding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified total 3 004 lncRNAs in cassava under normal or cold-treated conditions from Iso-seq data. We further characterized a lincRNA, CRIR1, as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Overexpression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulates a range of cold stress-related genes in a CBF-independent pathway. We further found that CRIR1 RNA can interact with MeCSP5, a homolog of the cold shock protein that acts as RNA chaperones, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of mRNA. In summary, our study greatly extends the repertoire of lncRNAs in plants as well as its responding to cold stress. Moreover, it reveals a sophisticated mechanism by which CRIR1 regulates plant cold stress response by modulating the expression of stress-responsive genes and increasing the translational yield.

Global identification of long non-coding RNAs involved in the induction of spinach flowering

Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.

Small proteins in Archaea, a mainly unexplored world

In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome wide approaches.

Self-Transcendent Emotions and Their Social Effects: Awe, Elevation and Kama Muta Promote a Human Identification and Motivations to Help Others

Abundant literature shows the effects of negative emotions on motivations to engage in collective action (i.e., to collectively mobilize personal resources to achieve a common objective), as well as their influence on the creation of shared identities. In this proposal, we focus on the possible role of Self-Transcendent Emotions (STEs) defined as positive-valence emotions that have been key in the creation and maintenance of collective identities, as well as in promoting individuals well-being. In detail, we examine their influence in (a) strengthening a global identification, (b) increasing willingness to collectively help others, and (c) improving people’s wellbeing. For this reason, we conducted a preliminary literature review of k = 65 independent studies on the effects of STEs on connection to others. Through this review (fully available in Supplementary Materials), we selected a sample of STEs (Awe, Elevation, and Kama Muta) and elicitors to conduct a video-base study. In it, 1,064 university students from 3 different cultural regions (from Spain and Ecuador) were randomized to answer one of three STE scales (i.e., each measuring one of the selected STEs), and evaluate three videos in random order (i.e., each prototypical for the selected STEs). Participants also answered a measure of global identification and intentions to collectively help others (after each video), as well as self-transcendent and well-being (at the end of the survey). Results from SEM analyses show these STEs motivated a fusion of identity with all humanity, as well as collective intentions to help others, even controlling for individuals’ value orientations. In addition, the three of them indirectly increased participants’ well-being through a higher global identity. While there are differences among them, these three STEs share common elements and their effects are constant across the different cultural regions. It is concluded that Awe, Elevation, and Kama Muta, even individually experienced, have a significant potential to influence people’s behavior. Specifically, in various forms of collective action aimed at helping others.

Global Identification of C2 Domain Contain Proteins And Characterization Of Genetic Variations For Involved Abiotic Stress Tolerance In Rice (Oryza sativa L.)

BackgroundC2DPs (C2 domain contain proteins) have been identified in different genomes that contain single or multiple C2 domains in their C or N-terminal, it possesses higher functional activity in the cell membrane between the cytoplasm and nucleus. Despite the identification of MCTPs and NTMC2s in rice, Arabidopsis, and cotton in a previous study, however, the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is unclear.ResultsIn this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. Synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genome of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely expressed in diverse tissues and were extensively involved in phytohormones and abiotic stress in rice. Prediction of the miRNA targets of OsC2DPs revealed that some of the homolog genes were regulated by consistent miRNAs and may carry out redundancy function. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of SNP genotyping and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 possessed diverse haplotypes for impacted cold tolerance owing to genomic variations.ConclusionsThese findings provide a comprehensive sight for characterized OsC2DPs in rice and their roles for abiotic stress. Further, the genetic variation supports the theoretical reference for molecular breeding in rice.