Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets

Abstract

Chinese mitten crab (CMC) or Eriocheir sinensis is a strong osmoregulator that can keep rigorous cellular homeostasis. CMC can flourish in freshwater, as well as seawater, habitats and represents the most important species for freshwater aquaculture. Salt stress can have direct effects on several stages (e.g., reproduction, molting, growth, etc.) of the CMC life cycle. To get a better overview of the genes involved in the gills of CMC under different salinity conditions, we conducted an RNA-Seq meta-analysis on the transcriptomes of four publicly available datasets. The meta-analysis identified 405 differentially expressed transcripts (DETs), of which 40% were classified into various transporter classes, including accessory factors and primary active transporters as the major transport classes. A network analysis of the DETs revealed that adaptation to salinity is a highly regulated mechanism in which different functional modules play essential roles. To the best of our knowledge, this study is the first to conduct a transcriptome meta-analysis of gills from crab RNA-Seq datasets under salinity. Additionally, this study is also the first to focus on the differential expression of diverse transporters and channels (transportome) in CMC. Our meta-analysis opens new avenues for a better understanding of the osmoregulation mechanism and the selection of potential transporters associated with salinity change.

Keywords: Chinese mitten crab; Eriocheir sinensis; RNA-Seq; gills; meta-analysis; osmoregulation; salinity; transcriptome; transporters; transportome.

Figure 1

Venn diagram showing the number of differentially expressed transcripts identified from individual studies and meta-analysis based on the Fisher method.

Figure 2

Heatmap showing differentially expressed transcripts identified by meta-analysis in the gills transcriptome of four different Chinese mitten crab (CMC) datasets under salinity. Only transcripts with an average fold change (FC) of ≥2.0 and a Benjamini-Hochberg adjusted p-value of <0.05 were considered to be differentially expressed.

Figure 3

Top 20 up- and downregulated differentially expressed transcripts.

Figure 4

Gene ontology (GO) enrichment of differentially expressed transcripts identified by the meta-analysis. Only the top 10 processes for each GO category in terms of the biological process (BP), molecular function (MF), and cellular component (CC) are shown. A complete list of enriched terms is provided as Table S4.

Figure 5

Community analysis of the interaction network. Red, green, and cyan nodes represent up- (square), downregulated (circle), and STRING-predicted (diamonds) genes, respectively. Nodes in purple indicate the hub genes labeled with orange text. The topmost enriched KEGG pathways (red text), GO terms (green text), and transporter class (pink text) are mentioned for each cluster. Clusters with <10 nodes (blue text) were excluded from the analysis.

Figure 6

Classification of differentially expressed transcripts into various types of transporters at the (A) class, (B) subclass, and (C) family levels, as described in the Transporter Classification Database (TCDB) system.