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Front. Genet. | doi: 10.3389/fgene.2019.00845

Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Response of the Pacific white shrimp, Litopenaeus vannamei

 Xiaoxi Zhang1, 2, 3,  Jianbo Yuan1, 2*,  Xiaojun Zhang1, 2, Chengzhang Liu1, 2, 4,  Jianhai Xiang1, 2 and  Fuhua Li1, 2*
  • 1Key Laboratory of Experimental Marine Biology, Institute of Oceanology (CAS), China
  • 2Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China
  • 3Chinese Academy of Sciences, China
  • 4Center for Ocean Mega-Science, Chinese Academy of Sciences, China

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 PCR 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 challenge. Specifically, type 2 AS genes under biotic stresses were mainly enriched in 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.

Keywords: Alternative splicing (AS), stress response, Litopenaeus vannamei, RNA-Seq, genome wide

Received: 07 May 2019; Accepted: 14 Aug 2019.

Edited by:

Jianke Li, Institute of Apiculture Research (CAAS), China

Reviewed by:

Rogerio R. Sotelo-Mundo, Centro de Investigación en Alimentación y Desarrollo (CIAD), Mexico
Cheng Sun, Institute of Apiculture Research (CAAS), China
Keyong Jiang, Institute of Oceanology, Chinese Academy of Sciences, China  

Copyright: © 2019 Zhang, Yuan, Zhang, Liu, Xiang and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Jianbo Yuan, Key Laboratory of Experimental Marine Biology, Institute of Oceanology (CAS), Qingdao, 266071, Shandong Province, China,
Prof. Fuhua Li, Key Laboratory of Experimental Marine Biology, Institute of Oceanology (CAS), Qingdao, 266071, Shandong Province, China,