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Tomato ( Lycopersicum esculentum L.) and pepper ( Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam.

Tobacco mosaic virus (TMV) is one of the most economically damaging plant viruses because of its wide host range and transmission mode. TMV manipulates the plant to produce viral proteins, instead of resistant ones. However, microbes with pathogenic defenses have been beneficial against the biotic stress caused by TMV. Through DNA metabarcoding, the microbe communities between parts of the phyllosphere and rhizosphere infected by TMV were compared over a two-week period. Overall, there was a variation of microbial presence and higher species richness in the mock-inoculated than viral inoculated plants. After one week, the mock inoculated plant organs had higher species richness than viral inoculated plant organs due to the presence of viral threat. After two weeks, the viral inoculated soil had the second highest species richness due to the soil being colonized and the presence of defense mechanisms. In addition, there was a wide range of taxa present such as Proteobacteria, Bacteroidetes, Acidobacteria, and Cyanobacteria. [ABSTRACT FROM AUTHOR]

We have developed an efficient method to rapidly generate infectious inoculum of a plant RNA virus and confirmed its infectivity by mechanical inoculation. The method takes advantage of overlap PCR to bypass the cloning steps, which makes it relatively simple, rapid, and inexpensive compared to the traditional methods. Using this approach, inoculum of a tobamovirus, Turnip vein clearing virus (TVCV), was generated. PCR products specific for the 35S promoter and TVCV genome were used as templates for overlap PCR to form a single product containing the full-length TVCV cDNA under the control of the double 35S promoter, and the entire process took only 8 h. This inoculum was infectious in Nicotiana benthamiana , and its infectivity was ca. 67% compared to 0% and 100% with negative and positive controls, respectively. Thus, this rapid method generates efficient infectious inoculum for a plant RNA virus. • Fusion of 35S promoter and TVCV was rapidly created by overlap PCR. • Infectivity of the fusion construct was confirmed by mechanical inoculation in Nicotiana benthamiana. • A recombinant TVCV expressing GFP was rapidly generated by our method. [ABSTRACT FROM AUTHOR]

Highlights: [•] We developed a method for screening of plant NBS-LRR genes that confer a HR. [•] The transient expression of the R gene induced local HR upon infection of virus. [•] Transcribed viral RNA can be used as an alternative to viral sap for HR induction. [•] An R gene that confers HR to the potyvirus Pepper mottle virus was identified. [ABSTRACT FROM AUTHOR]