Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus

Abstract

Environmental salinity is an important abiotic factor influencing normal physiological functions and productive performance in the sea cucumber Apostichopus japonicus. It is therefore important to understand how changes in salinity affect sea cucumbers in the face of global climate change. In this study, we investigated the responses to salinity stress in sea cucumbers using mRNA and miRNA sequencing. The regulatory network of mRNAs and miRNAs involved in salinity stress was examined, and the metabolic pathways enriched for differentially expressed miRNAs and target mRNAs were identified. The top 20 pathways were involved in carbohydrate metabolism, fatty acid metabolism, degradation, and elongation, amino acid metabolism, genetic information processing, metabolism of cofactors and vitamins, transport and catabolism, and environmental information processing. A total of 22 miRNAs showed differential expression during salinity acclimation. The predicted 134 target genes were enriched in functions consistent with the results of gene enrichment based on transcriptome analysis. These results suggested that sea cucumbers deal with salinity stress via changes in amino acid metabolism, ion channels, transporters, and aquaporins, under stimulation by environmental signals, and that this process requires energy from carbohydrate and fatty acid metabolism. Salinity challenge also induced miRNA expression. These results provide a valuable genomic resource that extends our understanding of the unique biological characteristics of this economically important species under conditions of salinity stress.

Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

“…Small RNA libraries were constructed and sequenced by a high-throughput sequencing method (on an Illumina HiSeq 2500 platform) at Novogene (Beijing, China), according to previously published methods [53]. Quality control and analysis of sequencing data were also performed by Novogene using methods described previously [54,55]. The miRBase (version 22) was used as a reference to search for known miRNAs by software miRDeep2, and srna-tools-cli was used to obtain the potential miRNAs and draw the secondary structures [56].…”

Identification and characterization of miRNAs and target genes response to hypoosmotic adaption in the cobia, Rachycentron canadum

“…A total of 548 miRNA were identified during low-salinity adaptation, and 22 miRNAs were significantly up-regulated and 34 were significantly down-regulated, indicating that miRNAs are differentially regulated to deal with hypoosmotic stress by R. canadum. Previous studies have shown that miRNAs are widely involved in the adaptation of salinity change in fish and other species via silencing complexes, which can lead to cleavage of target genes or inhibition of translation of the target genes (Flynt et al, 2009;Tian et al, 2019;Zhao et al, 2016).…”

“…It is widely known that miRNAs play important roles in many biological processes, such as signal transduction, organ development, immunity, tumorigenesis, metabolism, cell proliferation and apoptosis and so on (Deng et al, 2016;Jung et al, 2019;Lin et al, 2020;Png et al, 2012;Suzuki, 2018;Tian et al, 2019;Yuan et al, 2015).…”

“…Since there was no publicly available information of R. canadum genome, the target gene prediction was based on the assembled unigenes from the R. canadum RNA-seq and annotation information (SRP202920). The candidate target genes of DEMs were predicted using RNAhybrid 2.1.2 + svm_light 6.01 package, miRanda 3.3a algorithm and TargetScan 7.0 software, and the intersection of the predicted results obtained was taken as the most potential predicted results of the miRNA target genes (Tian et al, 2019). The default parameters of three software were set as free energy >−10 kcal/mol and score >140.…”

GC‐MS‐based metabolomics reveal that light intensity during indoor overwintering affects the metabolism of Scylla paramamosain

“…Metabolic processes allow organisms to grow and reproduce, maintain their structure, and respond to the external environment. Changes in metabolic patterns among environments are typically related to the pathways of energy production and consumption, including the amino acid metabolism, the carbohydrate metabolism, the fatty acid metabolism, the nucleotide metabolism, membrane transport, protein synthesis and protein digestion (Abdel‐Tawwab & Wafeek, 2017; Das & Majhi, 2015; Tian et al., 2019; Younis, 2015). Thus, changes in the abundance of various metabolites can help to clarify the energy changes associated with different light intensities.…”