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Tissue-Specific Analysis of Alternative Splicing Events and Differential Isoform Expression in Large Yellow Croaker (Larimichthys crocea) After Cryptocaryon irritans Infection

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Abstract

The large yellow croaker (Larimichthys crocea) is one of the most important mariculture fish in China. Recently, cryptocaryonosis caused by Cryptocryon irritans infection has brought huge economic losses and threatens the healthy and sustainable development of the L. crocea industry. However, the molecular mechanism and regulation process for L. crocea resistance to C. irritans infection has not been fully researched. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism that allows cells to produce transcriptional and proteomic diversity. The results of AS are tissue dependent, and the expression of tissue-specific transcription subtype genes is determined by AS and transcriptional regulation. However, studies on the tissue specificity of AS events in L. crocea following infection with C. irritans have not been performed. In this study, the L. crocea were artificially infected with C. irritans; their skin and gill were collected at 0 h, 24 h, 48 h, 72 h, and 96 h post infection. After sequencing and differential expression analysis, a set of 452, 692, 934, 711, 534, and 297 differential alternative splicing (DAS) events were identified in 0 h, 12 h, 24 h, 48 h, 72 h, and 96 h post infection respectively. Furthermore, 4160 differentially expressed isoforms (DEIs) and 4209 DEI genes were identified from all time point groups. GO enrichment and pathway analysis indicated that many genes of DAS and DEIs were rich in immune-related GO terms and KEGG pathways, such as the Toll and Imd signaling pathway, NOD-like receptor signaling pathway, TNF signaling pathway, and TNF signaling pathway. Among hub DEI genes, alternative splicing-related genes (cwc25, prpf8, and sf3a3), skin function-related gene (fa2h), and oxygen deprivation-related gene (hyo1) were found in DEI genes. This study provided insight into the temporal change of DAS and DEIs between skin and gill of L. crocea against C. irritans infection and revealed that these differences might play immune-related roles in the infection process.

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Acknowledgements

This work was supported by the Fundamental Research Funds for the Central Universities [20720200110], the National Natural Science Foundation of China [U21A20264], the Special Foundation for Major Research Program of Fujian Province [2020NZ08003], the Local Science and Technology Development Project Guide by The Central Government [2019L3032], the Open Research Fund Project of State Key Laboratory of Large Yellow Croaker Breeding [LYC2019RS02, LYC2019RS03], the China Agriculture Research System [CARS-47], and the “Science and Technology Innovation 2025” Major Special Project of Ningbo City [No. 2021Z002].

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  1. Ang Qu and Yulin Bai contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China

    Ang Qu, Yulin Bai, Xinyi Zhang, Junjia Zeng, Fei Pu, Linni Wu, Peng Xu & Tao Zhou

  2. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China

    Peng Xu & Tao Zhou

  3. Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China

    Peng Xu & Tao Zhou

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Contributions

ZT and PX conceived and supervised the study. AQ, YB, and ZT designed and managed the experiments, and wrote the manuscript. AQ, YB, and XZ performed the analysis and designed the charts and Tables. AQ, YB, XZ, JZ, FP, and LW conducted the experiments. All authors have read and approved the manuscript.

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Correspondence to Tao Zhou.

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Supplementary file6 (TIF 18625 KB). Fig S1. The percentage of each type of DAS events at each timepoint.

10126_2022_10133_MOESM7_ESM.tif

Supplementary file7 (TIF 7378 KB). Fig S2 The amount of GOterms in DAS genes varied over time in biological process, cellular component,and molecular function.

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Qu, A., Bai, Y., Zhang, X. et al. Tissue-Specific Analysis of Alternative Splicing Events and Differential Isoform Expression in Large Yellow Croaker (Larimichthys crocea) After Cryptocaryon irritans Infection. Mar Biotechnol 24, 640–654 (2022). https://doi.org/10.1007/s10126-022-10133-z

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