Comprehensive analyses of gene expression and alternative splicing to partially reveal the mechanism of crowding stress-inhibited intestinal development of largemouth bass (Micropterus salmoides)

Crowding stress (CS) is an inevitable abiotic stressor in intensified aquaculture, known to significantly impair fish species by compromising their growth performance. Our study indicated that CS hindered both the growth performance and intestinal development of largemouth bass. The growth performance of fish species is intricately linked to their intestinal development. To explore the underlying mechanism, we conducted a transcriptome analysis to elucidate the detrimental impact of crowding stress on intestinal development in largemouth bass (Micropterus salmoides). We identified a total of 330 differentially expressed genes (DEGs) in the CS group. Subsequent gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that a majority of these DEGs were significantly enriched in the cell cycle process (P < 0.05). Among the cell cycle-related DEGs, 4 were up-regulated (e.g. mat1a and soat1) and 58 were down-regulated (e.g. ccnb1, cenpe and espl1). Additionally, we discovered 473 differentially alternatively spliced (DAS) genes through alternative splicing analysis in the CS group. Among these DAS genes, cntrl, ddx3xb, e2f4, akt1, npat, myb and LOC119914646 were associated with the regulation of cell cycle. The findings were validated through RT-qPCR, confirming the reliability of our bioinformatics analysis. In conclusion, our research has confirmed the adverse impact of crowding stress on the cell cycle process in the intestines of largemouth bass. The genes identified in this study will contribute to a deeper understanding of the mechanisms underlying the inhibition of intestinal development caused by crowding stress.