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Sci Rep. 2018 Feb 19;8(1):3273. doi: 10.1038/s41598-018-21190-7.

Characterization of viral RNA splicing using whole-transcriptome datasets from host species.

Zhou C1,2,3, Liu S2,3,4, Song W2,3, Luo S5, Meng G2,3, Yang C2,3, Yang H1, Ma J2,3, Wang L6, Gao S6, Wang J2,7, Yang H2,7, Zhao Y8, Wang H9,10,11, Zhou X12,13.

Author information

1
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
2
BGI-Shenzhen, Shenzhen, 518083, China.
3
China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
4
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
5
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
6
CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China.
7
James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China.
8
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China. zhaoyun@scu.edu.cn.
9
BGI-Shenzhen, Shenzhen, 518083, China. huiwang789@gmail.com.
10
China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. huiwang789@gmail.com.
11
The Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK. huiwang789@gmail.com.
12
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China. xinzhou@cau.edu.cn.
13
National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing, 100193, China. xinzhou@cau.edu.cn.

Abstract

RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses.

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