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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
Source PublicationMARINE BIOTECHNOLOGY
Volume18Issue:5Pages:598-609
SubtypeArticle
AbstractAlternative 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.
KeywordAlternative Splicing Rna-seq Crassostrea Gigas Hsp60 Hsp90
DOI10.1007/s10126-016-9720-x
Indexed BySCI
Language英语
WOS IDWOS:000388831000007
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/136235
Collection海洋生物技术研发中心
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
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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