Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
| 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
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| 2019-09-12 | |
| 发表期刊 | FRONTIERS IN GENETICS
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| 卷号 | 10页码:11 |
| 通讯作者 | Yuan, Jianbo(yuanjb@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn) |
| 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. |
| 关键词 | alternative splicing (AS) stress response Litopenaeus vannamei RNA-seq genome-wide identification |
| DOI | 10.3389/fgene.2019.00845 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 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] ; 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 |
| WOS类目 | Genetics & Heredity |
| WOS记录号 | WOS:000485228100001 |
| 出版者 | FRONTIERS MEDIA SA |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/162781 |
| 专题 | 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, 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 |
| 第一作者单位 | 中国科学院海洋研究所 |
| 通讯作者单位 | 中国科学院海洋研究所 |
| 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. |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Zhang-2019-Genome-wi（2837KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
| Genome-Wide Analysis（3009KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
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