Alternative splicing impacts the rice stripe virus response transcriptome

Shanshan Li; Wenbin Guo; Chen Wang; Yao Tang; Lulu Li; Hehong Zhang; Yanjun Li; Zhongyan Wei; Jianping Chen; Zongtao Sun

doi:10.1016/j.virol.2023.109870

Alternative splicing impacts the rice stripe virus response transcriptome

Virology. 2023 Oct:587:109870. doi: 10.1016/j.virol.2023.109870. Epub 2023 Aug 28.

Authors

Shanshan Li¹, Wenbin Guo², Chen Wang¹, Yao Tang¹, Lulu Li³, Hehong Zhang³, Yanjun Li³, Zhongyan Wei³, Jianping Chen⁴, Zongtao Sun⁵

Affiliations

¹ College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
² Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK.
³ State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
⁴ College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China. Electronic address: jianpingchen@nbu.edu.cn.
⁵ State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China. Electronic address: sunzongtao@nbu.edu.cn.

PMID: 37669612
DOI: 10.1016/j.virol.2023.109870

Abstract

Alternative splicing (AS) is an important form of post transcriptional modification present in both animals and plants. However, little information was obtained about AS events in response to plant virus infection. In this study, we conducted a genome-wide transcriptome analysis on AS change in rice infected by a devastating virus, Rice stripe virus (RSV). KEGG analysis was performed on the differentially expressed (DE) genes and differentially alternative spliced (DAS) genes. The results showed that DE genes were significantly enriched in the pathway of interaction with plant pathogens. The DAS genes were mainly enriched in basal metabolism and RNA splicing pathways. The heat map clustering showed that DEGs clusters were mainly enriched in regulation of transcription and defense response while differential transcript usage (DTU) clusters were strongly enriched in mRNA splicing and calcium binding. Overall, our results provide a fundamental basis for gene-wide AS changes in rice after RSV infection.

Keywords: Alternative splicing (AS); Differential transcript usage (DTU); Differentially alternative spliced (DAS); Differentially expressed genes (DEGs); Genome-wide; Rice stripe virus (RSV); Transcriptome.