Identification and characterization of miRNAs in the gills of the mud crab (Scylla paramamosain) in response to a sudden drop in salinity

Huan Wang,Changkao Mu,Chunlin Wang,Lei Tang,Junkai Lu,Hongling Wei

doi:10.1186/s12864-018-4981-6

Abstract

BackgroundThe mud crab (Scylla paramamosain) is a euryhaline and commercially important species. MiRNAs participate in the regulation of many physiological activities.ResultsThe miRNA transcriptome of the gills of S. paramamosain was used to investigate the expression profiles of miRNAs in response to a sudden drop in salinity. In total, seven known miRNAs and 43 novel miRNAs were identified, with 18 differentially expressed small RNAs. Fourteen thousand nine hundred fifty-one differentially expressed miRNAs target genes were screened by prediction. GO analysis of differentially expressed miRNAs target genes indicated that 578 genes associated with cellular processes, 523 associated with metabolic processes, and 422 associated with single-organism processes were the most strongly affected by a sudden drop in salinity from 23‰ to 3‰. KEGG pathway analysis showed 14 pathways were related to amino acid metabolism, which plays an important role in osmoregulation. Besides, several pathways were associated with starch and sucrose metabolism (ko00500), glycosaminoglycan degradation (ko00531), and galactose metabolism (ko00052).ConclusionsS. paramamosain regulated osmotic pressure and energy balance by regulating target genes to adapt to a sudden changes in salinity. These results provided a basis for further investigations of miRNA-modulating networks underlying the osmoregulation of S. paramamosain.

Highlights

The mud crab (Scylla paramamosain) is a euryhaline and commercially important species
On the basis of previous research, the miRNA transcriptome of the gills of S. paramamosain was examined under normal conditions (23‰ salinity) and stress conditions caused by a sudden drop in salinity (3‰) in this study. These results provide a basis for further investigations of miRNA-modulation of networks underlying osmoregulation of S. paramamosain
Bgiseq-500 sequencing of small RNAs To identify miRNAs of the mud crab in response to a sudden drop in salinity, small RNA libraries derived from the CK and LS groups were constructed and sequenced using the BGIseq-500 Generation Sequencing Platform

Summary

Introduction

The mud crab (Scylla paramamosain) is a euryhaline and commercially important species. MiRNAs participate in the regulation of many physiological activities. The commercially important mud crab Scylla paramamosain (Crustacea: Decapoda: Portunidae: Syclla De Hann) is widely distributed along the coasts of southern China and other Indo-Pacific countries [23, 43, 47]. Due to its rapid growth, large size, popularity amongst consumers, and high market value, S. paramamosain is becoming an important farmed fish along the southeast coast of China [52, 28]. Small noncoding ribonucleic acid (snRNA), which include microRNA (miRNA), small interfering RNA (siRNA), and Piwi-associated RNA (piRNA), has been isolated from a wide variety of plant and mammalian cells. Most studies have focused on miRNAs, which are 19–23 nucleotides (nt) in length and formed as a single strand of RNA and highly phylogenetically conserved across

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