Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

Mingge Ma,Gentu Wu,Miao Sun,Mingjun Li,Xianchao Sun,Jiang Du,Ling Qing,Ke Li

doi:10.1186/s12985-018-1044-1

Abstract

BackgroundTobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. It is interesting that TbCSV induced severe upward leaf curling in Nicotiana benthamiana, but in the presence of TbCSB, symptoms changed to be downward leaf curling. However, the mechanism of interactions between viral pathogenicity, host defense, viral-betasatellite interactions and virus-host interactions remains unclear.MethodsIn this study, RNA-seq was used to analyze differentially expressed genes (DEGs) in N. benthamiana plants infected by TbCSV (Y35A) and TbCSV together with TbCSB (Y35AB) respectively.ResultsThrough mapping to N. benthamiana reference genome, 59,814 unigenes were identified. Transcriptome analysis revealed that a total of 4081 and 3196 DEGs were identified in Y35AB vs CK (control check) and Y35A vs CK, respectively. Both GO and KEGG analyses were conducted to classify the DEGs. Ten of the top 15 GO terms were enriched in both DEGs of Y35AB vs CK and Y35A vs CK, and these enriched GO terms mainly classified into three categories including biological process, cellular component and molecular function. KEGG pathway analysis indicated that 118 and 111 pathways were identified in Y35AB vs CK and Y35A vs CK, respectively, of which nine and six pathways were significantly enriched. Three major pathways in Y35AB vs CK involved in metabolic pathways, carbon metabolism and photosynthesis, while those in Y35A vs CK were related to Ribosome, Glyoxylate and dicarboxylate metabolism and DNA replication. We observed that 8 PR genes were significantly up-regulated and 44 LRR-RLK genes were significantly differentially expressed in Y35A treatment or in Y35AB treatment. In addition, 7 and 13 genes were identified to be significantly changed in biosynthesis and signal transduction pathway of brassinosteroid (BR) and jasmonic acid (JA) respectively.ConclusionsThese results presented here would be particularly useful to further elucidate the response of the host plant against virus infection.

Highlights

Tobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China
The multiple resistance mechanisms against cotton leaf curl disease (CLCuD) were revealed by the transcriptome analysis based on an RNA-seq in a naturally immune cotton species (Gossypium arboreum) caused by CLCuD [7]
Overview of transcriptome sequencing To profile gene expression during virus infection, RNAseq libraries were constructed for the control- and virus-inoculated N. benthamiana plants. 5.76 GB clean bases data and 59,814 unigenes were obtained from nine samples

Summary

Introduction

Tobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. TbCSV is one of the most important pathogens causing leaf curl disease on tomato and tobacco, Viral infection is a complicated procedure involving in the interaction between viruses and host plants. RNA-seq is a recently developed approach to transcriptome profiling via deep-sequencing technologies, which provides a far more precise measurement of levels of transcripts and their isoforms than other methods [6]. This technique was widely applied in interpretation the interaction between virus infection and host plant. Several host genes were identified to be involved in different cellular and physiological processes during the infection of other viruses, including South African cassava mosaic virus (SACMV) [10], Tomato yellow leaf curl Sardinia virus (TYLCSV), Mungbean yellow mosaic India virus (MYMIV) [11, 12], and Chilli leaf curl virus (ChiLCV) [13]

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Results

Conclusion