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. 2024 Oct 17;14(20):3005.
doi: 10.3390/ani14203005.

Analysis of Differential Alternative Splicing in Largemouth Bass After High Temperature Exposure

Xianxian Zhao  1   2 , Yizhou Wang  1   2 , Zhenlu Wang  1 , Tianma Luo  1   2 , Jun Huang  3 , Jian Shao  1
Affiliations

Analysis of Differential Alternative Splicing in Largemouth Bass After High Temperature Exposure

Xianxian Zhao et al. Animals (Basel). .

Abstract

Temperature is one of the critical factors affecting the physiological functions of fish. With ongoing global warming, changes in water temperature have a profound impact on fish species. Alternative splicing, being a significant mechanism for gene expression regulation, facilitates fish to adapt and thrive in dynamic and varied aquatic environments. Our study used transcriptome sequencing to analyze alternative splicing in largemouth bass gills at 34 °C for 24 h. The findings indicated an increase in both alternative splicing events and alternative splicing genes after high temperature treatment. Specifically, the comparative analysis revealed a total of 674 differential alternative splicing events and 517 differential alternative splicing genes. Enrichment analysis of differential alternative splicing genes revealed significant associations with various gene ontology (GO) terms and KEGG pathways, particularly in immune-related pathways like necroptosis, apoptosis, and the C-type lectin receptor signaling pathway. These results emphasize that some RNA splicing-related genes are involved in the response of largemouth bass to high temperatures.

Keywords: differential alternative splicing; environmental stress; largemouth bass; transcriptome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Volcano plot of DEGs statistics between the control and high temperature treatment groups. Red and blue dots represent up-regulated and down-regulated genes, respectively.
Figure 2
Figure 2
Statistics of alternative splicing events in the control and high temperature treatment groups. The horizontal axis is the number of variable shears under that type of event and the vertical axis is the classification of variable shear events. (1) AE: alternative exon ends (5′, 3′, or both); (2) IR: intron retention; (3) MIR: multi-IR; (4) MSKIP: multi-exon SKIP; (5) SKIP: skipped exon; (6) TSS: alternative 5′ first exon (transcription start site); (7) TTS: alternative 3′ last exon (transcription terminal site); (8) XAE: approximate AE; (9) XIR: approximate IR; (10) XMIR: approximate MIR; (11) XMSKIP: approximate MSKIP; (12) XSKIP: approximate SKIP. Different colors represent different splicing events.
Figure 3
Figure 3
Number statistics of differential alternative splicing events and differential alternative splicing genes between the control and high temperature treatment groups.
Figure 4
Figure 4
GO enrichment analysis of differential alternative splicing genes in the control and high temperature treatment groups. The top 20 category terms of differential alternative splicing genes were enrich in the biological process (A), cellular component (B), and molecular function categories (C).
Figure 5
Figure 5
KEGG enrichment pathways of DAS genes.
Figure 6
Figure 6
Genes presented between differentially expressed genes and differentially spliced genes.
Figure 7
Figure 7
The atp2a1 gene analysis and RT-qPCR validation. (A) Percent spliced in of atp2a1X1 and atp2a1X2. (B) Relative mRNA expression level of atp2a1X1 and atp2a1X2. (C) RT-qPCR validation of DEGs.
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