Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

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.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1044-1) contains supplementary material, which is available to authorized users.

Suppression of nbe-miR1919c-5p Expression in Nicotiana benthamiana Enhances Tobacco Curly Shoot Virus and Its Betasatellite Co-Infection

“…benthamiana plants were grown in a greenhouse set at 24-26 • C and a 16/8-h (light/dark) light cycle. Three-week-old plants were inoculated with the two viruses as previously reported [23]. Briefly, A. tumefaciens cultures carrying an infectious TbCSV (isolate Y35) clone or an infectious TbCSB clone were 1:1 (v/v) ratio mixed and then infiltrated into the N. benthamiana leaves using needleless syringes as described in [24].…”

“…Total DNA was extracted from collected leaf samples using the cetyltrimethylammonium bromide (CTAB) method [25]. To determine the virus infection in the assayed plants, viral DNAs in young systemic leaves were detected through polymerase chain reaction (PCR) using TbCSV or TbCSB-specific primers [23]. To quantify viral DNA accumulation in the infected plants, we utilized a quantitative PCR (qPCR) methodology described before [26].…”

Diversity, Function and Regulation of Cell Surface and Intracellular Immune Receptors in Solanaceae

“…At the transcriptional level, tomato immune receptors have been found to be induced by ergosterol and squalene from the fungal symbiont Trichoderma [34]. In solanaceous plants, examples of RLP/RLK and NLR genes can be induced by wounding [35,36], hormone treatments [10,35,37], pathogen infection [10,[37][38][39][40] and effector gene expression [37,41]. In Arabidopsis, both RLP and NLR genes can be induced by a range of environmental stresses and different hormones [42,43].…”

Transcriptome reprogramming in the shoot apical meristem of CymRSV‐infected Nicotiana benthamiana plants associates with viral exclusion and the lack of recovery

“…). This experiment showed that after 3 days post‐inoculation (dpi) the virus is already present in the shoot, but the endogenous transcription of the housekeeping GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE ( GAPDH ) and the PATHOGENESIS-RELATED PROTEIN Q ( PRQ ) (Li et al ., ; Pesti et al , ) are unchanged. In contrast, after 4 dpi, in the virus‐invaded plant tissues close to the SAM, the GAPDH level is undetectable, while PRQ is greatly induced.…”