Transcriptome sequencing revealed the genes and pathways involved in salinity stress of Chinese mitten crab,Eriocheir sinensis

Abstract

A total of 276.9 million reads were obtained and assembled into 206, 371 contigs with an average length of 614 bp and N50 of 1,470 bp. Comparison of digital gene expression between treatment and control group reveals 1,151 and 941 genes were significantly differentially expressed in crab gill and muscle, respectively. In gill and muscle, protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, and mitochondria dysfunction pathways were the top pathways differentially expressed following the challenge. EIF 2 signaling pathway and IGF-1 signaling pathway were the top ones among the signal-related pathways. Most of the amino acid metabolism pathways were found to be involved in this process. The expression patterns of 15 differentially expressed genes were validated by quantitative real-time RT-PCR (average correlation coefficient 0.80). This is the first report of expression analysis of genes and pathways involved in osmoregulation of Eriocheir sinensis through transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanism of salinity stress adaptation for crustacean species.

Use of RNA-seq in Aquaculture Research

“…RNA-seq was also employed to understand the mechanism of osmoregulation in Asian seabass [8], Amur ide [9], and Chinese mitten crab [24]. For instance, protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, mitochondrial dysfunction EIF2 signaling, IGF-1 signaling, and amino acid metabolism were found to be the top stressrelated pathways in the Chinese mitten crab after ambient salinity challenge revealed by RNA-seq [24]. Similar studies were reported in white shrimp exposed to nitrite [25].…”

“…Similar work was also conducted to determine the heat stress-induced gene expression profile in channel catfish [22], zebrafish [23] and rainbow trout [7]. RNA-seq was also employed to understand the mechanism of osmoregulation in Asian seabass [8], Amur ide [9], and Chinese mitten crab [24]. For instance, protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, mitochondrial dysfunction EIF2 signaling, IGF-1 signaling, and amino acid metabolism were found to be the top stressrelated pathways in the Chinese mitten crab after ambient salinity challenge revealed by RNA-seq [24].…”

Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics

“…Here, we focus on the DEGs identified using edgeR since those most closely approximated numbers reported in previous studies (Li et al , 2014; Lv et al , 2013; Towle et al , 2011). Overall, a total of 477 DEGs were identified among the pairwise comparisons, relating to a wide variety of physiological processes (Fig.…”

“…These points are well-illustrated in a microarray examination of expression for 4462 genes in the green crab Carcinus maenas during salinity transfers (Towle et al , 2011), where upregulation of well-characterized ion transporters such as NKA was confirmed while revealing: 1) novel ion transporters (e.g., a Na + /glucose transporter) with expression patterns similar to NKA and CA; 2) no differential expression (DE) in stress genes, suggesting responses to changing salinity are a routine physiological process; 3) up-regulated mitochondrial biogenesis pathways, implying increased ATP demand in brackish waters, and; 4) upregulation of numerous genes lacking annotation. Recently, studies have employed RNA-Seq to examine salinity-mediated gene expression in the gills of decapods, often recovering thousands of DE genes, many belonging to functional groups not previously implicated in osmoregulation (e.g., chitin and amino acid metabolism) (Li et al , 2014; Lv et al , 2013). In spite of these advancements, the molecular basis underlying functional differences between the anterior and posterior gills of decapods remain poorly understood and have yet to be investigated at the transcriptomic level.…”

Identification and characterization of nascent polypeptide-associated complex alpha from Chinese mitten crab (Eriocheir sinensis): A novel stress and immune response gene in crustaceans

“…Dissecting the molecular determinants that respond both to stress and immune challenges thus is of a great interest to understand the crosstalk between stress and immunity in aquatic animals. Several genes and pathways involved in E. sinensis stress [3] and immune response [4] have been revealed by transcriptomic analysis, while the candidates that may participate in both stress adaptation and immune response remain largely uncharacterized. We have been perusing to identify the candidates that respond to stress and immune challenges in the Chinese mitten crabs and several candidate genes have been identified [5,6].…”