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Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster

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Abstract

Alternative splicing (AS) is thought to enhance transcriptome diversity dramatically and play an important role in stress adaptation. While well studied in vertebrates, AS remains poorly understood in invertebrates. Here, we used high-throughput RNA-sequencing data to perform a genome-wide survey of AS in the Pacific oyster (Crassostrea gigas), an economically important mollusk that is cultivated worldwide. This analysis identified 8223 AS events corresponding to 4480 genes in the Pacific oyster, suggesting that about 16 % of oyster multiexonic genes undergo AS. We observed that a majority of the identified AS events were related to skipped exons (37.8 %). Then Gene Ontology analysis was conducted to analyze the function of the genes that undergo AS and the genes that produce more than five AS isoforms. After that, the expression of AS isoforms facing temperature, salinity, and air exposure challenge were examined. To validate our bioinformatic-predicted results and examine whether AS affects stress adaptation, we selected heat-shock protein 60 (HSP60) and HSP90 genes, both of which experience AS, for reverse transcription PCR (RT-PCR). We also performed quantitative real-time PCR (qRT-PCR) to determine the relative expression of each AS isoform among different stress adapted populations. Our study indicates that AS events are likely complex in the Pacific oyster and may be related to stress adaptation. These results will complement the predicted gene database of C. gigas and provide an invaluable resource for future functional genomic studies on molluscs.

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Acknowledgments

This research was supported by Shandong Provincial Natural Science Foundation (ZR2013DQ010), National Natural Science Foundation of China (31530079), National Basic Research Program of China (973 Program, No.2010CB126402), the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-48), and Taishan Scholars Climbing Program of Shandong.

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Authors and Affiliations

  1. Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China

    Baoyu Huang, Linlin Zhang, Xueying Tang, Guofan Zhang & Li Li

  2. Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China

    Baoyu Huang & Li Li

  3. National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China

    Baoyu Huang, Linlin Zhang, Xueying Tang, Guofan Zhang & Li Li

  4. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China

    Xueying Tang & Guofan Zhang

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  1. Baoyu Huang
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  2. Linlin Zhang
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Correspondence to Li Li.

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Baoyu Huang and Linlin Zhang contributed equally to this work.

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Huang, B., Zhang, L., Tang, X. et al. Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster. Mar Biotechnol 18, 598–609 (2016). https://doi.org/10.1007/s10126-016-9720-x

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  • DOI: https://doi.org/10.1007/s10126-016-9720-x

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