Genetic structure analyses of the tomato-infecting crinivirus Tomato chlorosis virus indicates low genetic variability in the p22 gene and evidence of segregation based on sampling location in Brazil

Abstract

One of the most important virus diseases in tomatoes in Brazil is caused by isolates of tomato chlorosis virus (ToCV, Tomato chlorosis virus, genus Crinivirus, family Closteroviridae). ToCV has a bipartite genome which is encapsidated in filamentous particles. RNA1 encodes an RNA silencing suppressor, the protein p22, that has been described as a highly variable region for members of the family. Here, we examined the genetic variability of the p22 gene in ToCV isolates from tomato plants collected from three different geographical regions of Brazil and compared them with other data sets representing the ToCV p22 population from South Korea and Spain. A low genetic diversity was found for the ToCV p22 gene, and negative selection was likely predominant in all analyzed populations. In a phylogenetic analysis, the Brazilian isolates form a monophyletic group with strong evidence of population structuring based on sampling location. Our results indicate a possibility, in the future, for the emergence of ToCV subpopulations with specific genetic characteristics that reflect the conditions of the ecological niche where they are inserted.