Whole Transcriptome Analysis Reveals the Global Molecular Responses of mRNAs, lncRNAs, miRNAs, circRNAs, and Their ceRNA Networks to Salinity Stress in Hong Kong Oysters, Crassostrea hongkongensis.

The Hong Kong oyster, Crassostrea hongkongensis, is an estuarine bivalve with remarkable commercial value in South China, and the increase of salinity in estuaries during the dry season has posed a major threat to the oyster farming. To explore the global transcriptional response to salinity stress, a whole-transcriptome analysis was performed with the gills of oysters in 6‰, 18‰, and 30‰ filtered seawater. Overall, 2243, 194, 371, and 167 differentially expressed mRNAs (DEmRNAs), differentially expressed long non-coding RNAs (DElncRNAs), differentially expressed circular RNAs (DEcircRNAs), and differentially expressed microRNAs (DEmiRNAs) were identified, respectively. Based on GO enrichment and KEGG pathway analysis, these important DEmRNAs, DElncRNAs, DEcircRNAs, and DEmiRNAs were predicted to be mainly involved in amino acids metabolism, microtubule movement, and immune defense. This demonstrated the complexity of dynamic transcriptomic profiles of C. hongkongensis in response to salinity fluctuation. The regulatory relationships of DEmiRNAs-DEmRNAs, DElncRNAs-DEmiRNAs, and DEcircRNAs-DEmiRNAs were also predicted, and finally, a circRNA-associated competing endogenous RNA (ceRNA) network was constructed, consisting of six DEcircRNAs, eight DEmiRNAs, and five DEmRNAs. The key roles of taurine and hypotaurine metabolism and phenylalanine metabolism were highlighted in this ceRNA network, which was consistent with the major contribution of free amino acids to intracellular osmolality and cell volume regulation. Collectively, this study provides comprehensive data, contributing to the exploration of coding and non-coding RNAs in C. hongkongensis salinity response. The results would benefit the understanding of the response mechanism of bivalves against salinity fluctuation, and provide clues for genetic improvement of C. hongkongensis with hyper-salinity tolerance.

The complete mitogenome of giant freshwater prawn (Macrobrachium rosenbergii) from two different selective breeding populations in China.

The giant freshwater prawn (GFP), Macrobrachium rosenbergii, is one of the largest freshwater shrimps in the world, being widely cultured because of its high economic value. In this study, complete mitogenomes of two GFP individuals from different selective breeding populations, 'South Taihu No.2' (ST) and 'Shufeng' (SF), were newly sequenced, compared with each other, and with those of other published Macrobrachium species. The total length is 15,767 bp (ST) and 15,766 bp (SF), including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region. The phylogenetic analyses based on whole mitogenome sequences suggest that 'Shufeng' has a slightly distant relationship with 'South Taihu No.2', with a pairwise genetic distance of 0.011. This study can provide a genetic background for the GFP selective breeding, and add significantly to the knowledgebase regarding crustacean biology and aquaculture as well.