Genetic variation and molecular evolution of tomato yellow leaf curl China virus and its betasatellite DNA isolates in China

Abstract Tomato yellow leaf curl China virus (TYLCCNV) and its betasatellite DNA isolates (TYLCCNB), seriously threaten tomato crop production in China. The present work aimed to analyze the genetic diversity and population structure of TYLCCNV/TYLCCNB, collected from 168 leaf samples with apparent yellow and curly leaf disease symptoms in China. The study involves phylogenetic, recombination, and selection pressure analysis, based on the genome sequences of 57 TYLCCNV and 109 TYLCCNB isolates. It was found that the TYLCCNV/TYLCCNB populations collected from the same geographic regions exhibit a close relationship under phylogenetic analysis. The recombination analysis revealed 8 possible recombination sites in the TYLCCNV C1 and C4 genes, and 6 possible recombination sites in the TYLCCNB βC1 gene. The results showed that the TYLCCNV C4 gene was under positive selection pressure in the selection pressure analysis. Moreover, nucleotide and predicted amino acid sequence identities in C1 and C4 were significantly lower than other ORF region sequences. The lower gene flow and significant genetic differentiation between the geographic populations of Guangxi and Sichuan provinces suggested that environmental adaptation was an important evolutionary force in shaping the genetic structure of TYLCCNV/TYLCCNB. In addition, C1 and C4 ORFs of TYLCCNV were proved to be the major mutation regions in greenhouse and field inoculation experiments. A-rich region was the major mutant hot spot in the associated betasatellites such as TYLCCNB, TbCSB, and MYVB. A thorough investigation into the evolutionary factors affecting the population structure of TYLCCNV/TYLCCNB will provide vital information for systematic virus management.