Genetic Variability and Molecular Evolution of Tomato Mosaic Virus Populations in Three Northern China Provinces

Abstract

RNA viruses tend to mutate during transmission and host infection, which is critical to viral adaptation and evolution. Tomato mosaic virus (ToMV) is a member of the genus Tobamovirus (family Virgaviridae) and an economically important virus with detrimental effects on tomatoes worldwide. Although the ToMV gene sequences have been completed in China, their genetic diversity and population structure remain unclear. We collected 425 tomato samples from tomato-growing areas in three northern Chinese provinces 2016. Reverse transcription PCR results showed that the average incidence of the virus in the field samples was 67.15%, and ToMV was detected in all test areas. The analysis of ToMV single nucleotide polymorphisms in China showed that ToMV was evolutionarily conserved, and the variation in the whole genome was uneven. Pairwise identity analysis showed significant variability in genome sequences among ToMV strains with genomic nucleotide identities of 73.2–99.6%. The ToMV population in the northern Chinese provinces had purification and selection functions, which were beneficial in the evolution of the ToMV population. Although there has been some distribution of ToMV strains in China, the virus was generally stabilized as a uniform strain under the pressure of purification selection. Our findings show how to monitor the prevalent strains of ToMV and their virulence in China and provide useful information for its prevention and control.

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

“…The phylogenetic analysis provides insights into the global diversity of ToMV strains. The majority of the strains cluster within a primary clade, which is consistent with the findings reported by Lyu et al [ 34 ]. Notably, the isolates INIFAP JM1–3 form a distinct group.…”

“…For ToMV, the 3′ end was additionally amplified with RT-PCR and Sanger sequencing. The RT-PCR was performed on each of the 36 samples using the specific direct primer ToMV_GSPD1 (5′-GGTTGCAATTCGGTCTGCTAT-3′) designed from the assembled contigs and the reverse primer ToMV_3R from the study by Lyu et al [ 34 ], with a 16 (T > A) base substitution (3′-TTATATATGGGCCCCTACCG-5′). These primers flank a 124 nt region of the coat protein (CP) end and the complete 3′ untranslated region (UTR) of ToMV.…”

Dissecting Diagnostic and Management Strategies for Plant Viral Diseases: What Next?

“…To determine the viral particle concentration in infected plants, researchers employ various methods. One approach involves infecting indicator plants and observing the development of mosaic-like or necrotic spots on their leaves, which vary depending on the viral species [28]. For instance, Nicotiana glutinosa L. leaves are used to identify and measure potato virus concentrations, while young tobacco plants (Nicotiana glutinosa) serve as indicators for tomato aspermy virus.…”