The caspase gene family in Micropterus salmoides: genome-wide characterization, bioinformatics, and expression profiling analysis

Apoptosis, a programmed cell death process mediated by caspases, is crucial for immunity and development. Caspases are categorized into initiator and effector types, regulating apoptosis via intrinsic and extrinsic pathways, and are also involved in pyroptosis and other cellular processes. In fish, diverse caspase genes have been identified and shown to participate in embryonic development and immune responses against bacterial infection. However, their role in largemouth bass against Aeromonas hydrophila—a pathogen causing severe intestinal inflammation and septicemia—remains unclear. This study identifies caspase genes in largemouth bass and investigates their expression and evolution post-infection, providing insights into their immune functions. This study presents the first comprehensive genomic analysis of caspases in largemouth bass, identifying 19 caspase genes: 3 inflammatory (caspase-1 orthologs), 6 effector (caspase-3/6/7), 8 initiator (caspase-2/8/9/10/20), and 2 unclassified (caspase-17) caspases. Functional and evolutionary analyses demonstrated a high level of homology between largemouth bass caspases and those of other teleosts. The sequence diversity analysis revealed that caspase genes in largemouth bass are subject to extensive mutational changes, predominantly through nonsynonymous single nucleotide variants, which may play a role in immune adaptation and resistance to disease. Alternative splicing analysis revealed multiple splicing sites and events in caspases of largemouth bass. Differential alternative splicing analysis showed significant induction of MsCASP8₁ variants after infection with Aeromonas veronii. Gene structure and sequence alignment analyses demonstrated that these isoforms result from alternative splicing events involving the 5th exon. Transcriptome profiling and qRT-PCR analyses revealed that most caspase genes in largemouth bass are responsive to Aeromonas hydrophila infection. This study systematically analyzed the characteristics of the caspase gene family in largemouth bass and identified associative patterns consistent with potential roles in innate immune responses, providing testable hypotheses for future functional validation. This study comprehensively identified the caspase gene family in largemouth bass, analyzing their genomic organization, evolutionary relationships, sequence diversity, alternative splicing patterns, and expression responses to Aeromonas hydrophila infection. The findings provide valuable insights for further investigation into caspase-mediated apoptosis and immune mechanisms in teleost fish under Aeromonas hydrophila stress.