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Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish

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Abstract

Alternative splicing is the process of generating multiple transcripts from a single pre-mRNA used by eukaryotes to regulate gene expression and increase proteomic complexity. Although alternative splicing profiles have been well studied in mammalian species, they have not been well studied in aquatic species, especially after biotic stresses. In the present study, genomic information and RNA-Seq datasets were utilized to characterize alternative splicing profiles and their induced changes after bacterial infection with Edwardsiella ictaluri in channel catfish (Ictalurus punctatus). A total of 27,476 alternative splicing events, derived from 9694 genes, were identified in channel catfish. Exon skipping was the most abundant while mutually exclusive exon was the least abundant type of alternative splicing. Alternative splicing was greatly induced by E. ictaluri infection with 21.9% increase in alternative splicing events. Interestingly, genes involved in RNA binding and RNA splicing themselves were significantly enriched in differentially alternatively spliced genes after infection. Sequence analyses of splice variants of a representative alternatively spliced gene, splicing factor srsf2, revealed that certain spliced transcripts may undergo nonsense-mediated decay (NMD), suggesting functional significance of the induced alternative splicing. Although statistical analysis was not possible with such large datasets, results from quantitative real-time PCR from representative differential alternative splicing events provided general validation of the bacterial infection-induced alternative splicing. This is the first comprehensive study of alternative splicing and its changes in response to bacterial infection in fish species, providing insights into the molecular mechanisms of host responses to biotic stresses.

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Funding

This project was supported by Agriculture and Food Research Initiative (AFRI) Competitive Grants (2015-67015-22975 and 2017-67015-26295) from the USDA National Institute of Food and Agriculture (NIFA), under the Animal Health Program, and the Animal Breeding, Genetics and Genomics Program. Suxu Tan was supported by a scholarship from the China Scholarship Council.

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  1. The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA

    Suxu Tan, Wenwen Wang, Xiaoxiao Zhong, Changxu Tian, Donghong Niu, Lisui Bao, Tao Zhou, Yulin Jin, Yujia Yang, Zihao Yuan, Dongya Gao & Rex Dunham

  2. College of Life Sciences, Shanghai Ocean University, Shanghai, China

    Donghong Niu

  3. Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA

    Zhanjiang Liu

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  1. Suxu Tan
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Tan, S., Wang, W., Zhong, X. et al. Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish. Mar Biotechnol 20, 729–738 (2018). https://doi.org/10.1007/s10126-018-9844-2

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