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Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster
Huang, Baoyu1,2,3; Zhang, Linlin1,3; Tang, Xueying1,3,4; Zhang, Guofan1,3,4; Li, Li1,2,3
2016-10-01
发表期刊MARINE BIOTECHNOLOGY
卷号18期号:5页码:598-609
文章类型Article
摘要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.
关键词Alternative Splicing Rna-seq Crassostrea Gigas Hsp60 Hsp90
DOI10.1007/s10126-016-9720-x
收录类别SCI
语种英语
WOS记录号WOS:000388831000007
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文献类型期刊论文
版本出版稿
条目标识符http://ir.qdio.ac.cn/handle/337002/136235
专题海洋生物技术研发中心
作者单位1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao, Peoples R China
3.Chinese Acad Sci, Inst Oceanol, Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao, Peoples R China
4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
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Huang, Baoyu,Zhang, Linlin,Tang, Xueying,et al. Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster[J]. MARINE BIOTECHNOLOGY,2016,18(5):598-609.
APA Huang, Baoyu,Zhang, Linlin,Tang, Xueying,Zhang, Guofan,&Li, Li.(2016).Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster.MARINE BIOTECHNOLOGY,18(5),598-609.
MLA Huang, Baoyu,et al."Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster".MARINE BIOTECHNOLOGY 18.5(2016):598-609.
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