Alternative splicing (AS) plays an important role in various physiological processes in eukaryotes, such as the stress response. However, patterns of AS events remain largely unexplored during salinity acclimation in fishes. In this study, we conducted AS analysis using RNA-seq datasets to explore splicing patterns in the gill tissues of rainbow trout exposed to altered salinity environments, ranging from 0 ‰ (T0) to 30 ‰ (T30). The results revealed 1441, 351, 483, 1051 and 1049 differentially alternatively spliced (DAS) events in 5 pairwise comparisons, including T6 vs. T0, T12 vs. T0, T18 vs. T0, T24 vs. T0, and T30 vs. T0, respectively. These DAS events were derived from 1290, 328, 444, 963 and 948 genes. Enrichment analysis indicated that these DAS genes were related to RNA splicing and processing. Among these, 14 DAS genes were identified as members of the large heterogeneous nuclear RNP (hnRNP) gene family. Alternative 3′ splice site (A3SS), exon skipping (SE) and intron retention (RI) events resulted in the fragmentation or even loss of the functional RNA recognition motif (RRM) domains in hnrnpa0, hnrnp1a, hnrnp1b and hnrnpc genes. The incomplete RRM domains would hinder the interactions between hnRNP genes and pre-mRNAs. It would in turn influence the splicing patterns and mRNA stability of downstream target genes in response to salinity changes. The study provides insights into salinity acclimation in gill tissues of rainbow trout and serves as a significant reference on the osmoregulation mechanisms at post-transcription regulation levels in fish.

选择性剪接（AS）在真核生物的各种生理过程中发挥着重要作用，例如应激反应。然而，在鱼类盐度驯化过程中，AS 事件的模式在很大程度上仍未被探索。在本研究中，我们使用 RNA-seq 数据集进行 AS 分析，以探索暴露于盐度变化环境（范围从 0 ‰（T0）到 30 ‰（T30）的虹鳟鱼鳃组织中的剪接模式。结果显示，5 次配对比较中存在 1441、351、483、1051 和 1049 个差异选择性剪接 (DAS) 事件，包括 T6 与 T0、T12 与 T0、T18 与 T0、T24 与 T0 以及 T30 与 T0 ， 分别。这些DAS事件源自1290、328、444、963和948基因。富集分析表明这些DAS基因与RNA剪接和加工相关。其中，14个DAS基因被鉴定为大型异质核RNP（hnRNP）基因家族的成员。选择性 3' 剪接位点 (A3SS)、外显子跳跃(SE) 和内含子保留 (RI) 事件导致hnrnpa0、hnrnp1a、hnrnp1b和hnrnpc基因中功能性 RNA 识别基序 (RRM) 结构域的片段化甚至丢失。不完整的 RRM 结构域会阻碍hnRNP基因和前 mRNA之间的相互作用反过来，它会影响下游靶基因响应盐度变化的剪接模式和 mRNA 稳定性。该研究为虹鳟鱼鳃组织的盐度驯化提供了见解，并为鱼类转录后调节水平的渗透调节机制提供了重要参考。