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Genetic Diversity Studies of Potato mop-top virus from Potato in the United States

Ying Zhai: Department of Plant Pathology, Washington State University

<div><em>Potato mop-top virus</em> (PMTV; Genus: <em>Pomovirus</em>; Family: <em>Virgaviridae</em>) is a soil-borne RNA virus that is becoming increasingly important in potato production in the US in recent years. This virus is transmitted by <em>Spongospora subterranea</em>. To understand the genetic diversity of the virus, the complete genome of six isolates of PMTV collected from different states in the USA were sequenced, analyzed, and compared with previously characterized isolate from the Washington State. The seven USA isolates showed high nucleotide similarities with one another in all seven genes. However, the nucleotide similarity of CPRT gene is least compared to the rest. The phylogenetic trees of the PMTV genes have some extent of similarity but are not dramatically consistent, with the RdRp gene (RNA 1) has the strongest divergence potential. Genetic diversity test showed that PMTV S strain to be more diverse than PMTV M strain and PMTV recombinant. Statistically significant and insignificant negative values of Tajima's D in PMTV S strain and M strain, respectively, suggest the dominance of purifying selection and population expansion is operating in those strains. The marginal likelihood mean substitution rate was 5.28x10<sup>-5</sup> subs/site/year, and 95% highest posterior density (HPD) substitution rate is between 5.29x10<sup>-5</sup> - 5.27x10<sup>-5</sup>. Our work provides the genomic basis for PMTV diagnosis, prevention, and disease epidemiology in the United States.</div>