Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei

doi:10.3389/fgene.2019.00845

CORC > 海洋研究所 > 中国科学院海洋研究所 > 实验海洋生物学重点实验室

	Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vannamei
	Zhang, Xiaoxi 2,3,4; Yuan, Jianbo 3,4; Zhang, Xiaojun 3,4; Liu, Chengzhang 1,3,4; Xiang, Jianhai3,4 ; Li, Fuhua 3,4
刊名	FRONTIERS IN GENETICS
	2019-09-12
卷号	10 页码:11
关键词	alternative splicing (AS) stress response Litopenaeus vannamei RNA-seq genome-wide identification
DOI	10.3389/fgene.2019.00845
通讯作者	Yuan, Jianbo(yuanjb@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
英文摘要	Alternative 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.
资助项目	National 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研究方向	Genetics & Heredity
语种	英语
出版者	FRONTIERS MEDIA SA
WOS记录号	WOS:000485228100001
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/162780]
专题	海洋研究所_实验海洋生物学重点实验室
通讯作者	Yuan, Jianbo; Li, Fuhua
作者单位	1.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Shandong, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Qingdao Natl Lab Marine Sci & Technol, Lab Menne Biol & Biotechnol, Qingdao, Shandong, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Shandong, Peoples R China
推荐引用方式 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.