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

SIMPLE SUMMARY: Eriocheir sinensis is a freshwater crab and is considered as one of the most important cost-effective species for freshwater aquaculture. E. sinensis can grow in both freshwater and brackish waters. In order to adapt to this changing salinity, E. sinensis can regulate the osmotic concentration of its hemolymph. Additionally, studies have shown that gills are one of the most important tissues in osmoregulation. In this work, we performed the first meta-analysis of publicly available RNA-Seq datasets to identify differentially expressed genes in the gills under different salinity conditions. The results highlighted that many different types of transporters show altered expression because of salinity change. Some of these transporters may serve as novel or new biomarkers for osmoregulation. The findings of this work also suggest that cellular processes related to many morphological changes are also affected. 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.