miRNA-seq provides novel insight into the response to hyper- and hypo- salinity acclimation in Crassostrea hongkongensis

• Published in: Gene 2024-10, Vol.924, p.148555, Article 148555
• Main Authors: Yan, Xueyu, Wei, Pinyuan, Zhang, Xingzhi, Guan, Junliang, Li, Wei, Zhang, Li, Zheng, Yusi, Chen, Yongxian, Zhu, Peng, He, Pingping, Peng, Jinxia
• Format: Article
• Language: English
• Subjects: acclimation; China; Crassostrea hongkongensis; estuaries; genes; littoral zone; microRNA; MiRNA-seq; miRNAs; RT-qPCR; salinity; Salinity acclimation; signal transduction; species
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2024.148555

•A total of 51 known miRNAs and 95 novel miRNAs were identified from the nine small RNA libraries.•6 down-regulated DE miRNAs responded to the hypo-salinity stress.•1 up-regulated and 5 down-regulated DE miRNAs responded to the hyper-salinity stress.•931 and 768 potential target genes were respectively predicted from the hypo- and hyper-salinity stress.•Genes involved in the vesicle-mediated transport and metal ion binding responded to the hypo-salinity stress.•Genes related to the signal transduction and metabolic process responded to the hyper-salinity stress. The Hong Kong oyster, Crassostrea hongkongensis, is a significant bivalve species with economic importance. It primarily inhabits the estuarine intertidal zones in southern China, making it susceptible to salinity fluctuations. Consequently, investigating the molecular mechanisms governing salinity regulation in C. hongkongensis is essential. In this study, we conducted miRNA-seq on C. hongkongensis to compare miRNA expression differences under varying salinities (5‰, 25‰, and 35‰). The miRNA sequencing revealed 51 known miRNAs and 95 novel miRNAs across nine small RNA libraries (S5, S25, and S35). Among these miRNAs, we identified 6 down-regulated differentially expressed (DE) miRNAs in response to hypo-salinity stress (5‰), while 1 up-regulated DE miRNA and 5 down-regulated DE miRNAs were associated with hyper-salinity stress (35‰). Additionally, we predicted 931 and 768 potential target genes for hypo- and hyper-salinity stress, respectively. Functional gene annotation indicated that the target genes under hypo-salinity stress were linked to vesicle-mediated transport and metal ion binding. Conversely, those under hyper-salinity stress were primarily involved in signal transduction and metabolic processes. These findings have provided insights into the regulatory role of miRNAs, their potential target genes and associated pathways in oyster hypo- and hyper-salinity stress, which establish a foundation for future studies on the roles of miRNAs in salinity acclimation mechanisms in C. hongkongensis.