Population genetic diversity of tomato spotted wilt orthotospovirus isolates from tobacco in Yunnan Province, China

We explored the genetic diversity and molecular evolutionary characteristics of tomato spotted wilt orthotospovirus (TSWV) on tobacco in Yunnan. In this study, 523 diseased tobacco leaf samples with suspected TSWV infection from nine different geographical sources in Yunnan were tested, and nucleocapsid protein (NP) of some isolates was amplified and cloned by reverse transcription-polymerase chain reaction (RT-PCR). Bioinformatics tools were used to analyze the population genetic structure and molecular evolutionary relationships of the tobacco TSWV population. TSWV was detected in 284 of 523 samples, with an average positivity rate of 54.3%. NP gene sequences of the 159 tobacco TSWV isolates obtained were all 777 bp, with 265 nucleic acid polymorphic sites, with 197 variant sites, including 66 parsimony informative and 131 single variant sites. Results for virus consistency and variation analysis based on the NP gene showed that the nucleotide sequence consistency of Yunnan TSWV isolates was 96 similar to 100%, the haplotype diversity 0.963, and the nucleic acid diversity 0.006. Phylogenetic analysis revealed that Yunnan tobacco TSWV isolates belong to the same group, with lower genetic differentiation and more frequent gene exchange among tobacco isolates of different geographical origins; their geographical characteristics were not obvious, and significant recombination signals were detected in the gene sequences of the DL-20 and DL-42 isolates. Many of the NP gene mutations of tobacco TSWV isolates from different geographic origins were deleterious in the nine different planting regions of Yunnan tobacco TSWV isolates, with only the population in the QJ planting region experiencing past population expansion events. The findings suggest that genetic recombination, mutation, and negative selection pressure are major drivers of the genetic diversity of tobacco TSWV in Yunnan. This study report of genetic variation in populations of TSWV isolates from various tobacco regions in Yunnan and provides information on the population structure of Yunnan tobacco TSWV isolates, which can help to prevent and control TSWV on Yunnan tobacco and provide a reference for research of disease-resistant varieties of tobacco.