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Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei
Zhang, Xiaoxi1,2,3; Yuan, Jianbo1,2; Zhang, Xiaojun1,2; Liu, Chengzhang1,2,4; Xiang, Jianhai1,2; Li, Fuhua1,2
2019-09-12
Source PublicationFRONTIERS IN GENETICS
Volume10Pages:11
Corresponding AuthorYuan, Jianbo(yuanjb@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
AbstractAlternative splicing (AS) can enhance transcript diversity dramatically and play an important role in stress adaptation. Limited researches of AS have been reported in the Pacific white shrimp (Litopenaeus vannamei), which is an important aquaculture species in the world. Here, we performed a genome-wide identification of AS events in L. vannamei based on eight transcriptomes. We identified 38,781 AS events in the shrimp genome, and some of them were validated by polymerase chain reaction experiments. These AS events correspond to 9,209 genes, accounting for 36% of protein-coding genes in the shrimp genome. The number of AS events increased after virus or bacteria infection and low salinity stress. Type 1 AS genes (AS was initially activated) were mainly enriched in substance and energy metabolism, such as carbon metabolism and amino metabolism. However, type 2 AS genes (AS events changed) displayed specific enrichment under different stress challenges. Specifically, type 2 AS genes under biotic stresses were mainly enriched in the pathogenic pathway and immune network, and the AS genes under low salinity stress were significantly enriched for betalain biosynthesis. In summary, our study indicates that AS events are complex in shrimp and may be related to stress adaptation. These results will provide valuable resource for functional genomic studies on crustaceans.
Keywordalternative splicing (AS) stress response Litopenaeus vannamei RNA-seq genome-wide identification
DOI10.3389/fgene.2019.00845
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31830100] ; National Natural Science Foundation of China[41776158] ; National Key R&D Program of China[2018YFD0900103] ; China Agriculture Research System-48[CARS-48]
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000485228100001
PublisherFRONTIERS MEDIA SA
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Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/162781
Collection实验海洋生物学重点实验室
Corresponding AuthorYuan, Jianbo; Li, Fuhua
Affiliation1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Shandong, Peoples R China
2.Chinese Acad Sci, Inst Oceanol, Qingdao Natl Lab Marine Sci & Technol, Lab Menne Biol & Biotechnol, Qingdao, Shandong, Peoples R China
3.Univ Chinese Acad Sci, Beijing, Peoples R China
4.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Shandong, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Zhang, Xiaoxi,Yuan, Jianbo,Zhang, Xiaojun,et al. Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei[J]. FRONTIERS IN GENETICS,2019,10:11.
APA Zhang, Xiaoxi,Yuan, Jianbo,Zhang, Xiaojun,Liu, Chengzhang,Xiang, Jianhai,&Li, Fuhua.(2019).Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei.FRONTIERS IN GENETICS,10,11.
MLA Zhang, Xiaoxi,et al."Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei".FRONTIERS IN GENETICS 10(2019):11.
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