The genetic structure and recombination analyses of Sweetpotato leaf curl virus (SPLCV) population in China

Sweetpotato leaf curl virus (SPLCV) is a species of virus that causes substantial yield losses in sweetpotato. In this study, twenty-four complete genomic sequences of SPLCV which identified from the sweetpotato samples collected from China, were calculated into four strains. A total of 11.9% isolates were recombinants, and ten recombination patterns were detected. In addition to C3 , V1 , IR and C1 genes, the both ends of the V2 gene were also identified as recombination hot spots for SPLCV. Negative (purifying) selection was identified among all six SPLCV genes, except for C4 gene was under the variety of choices (positive selection) for adaptive protein evolution. The mismatch distribution of SPLCV in all subgroups and groups was multiple peaked or ragged, indicating SPLCV population has existed for a long time. The gene flows between Shandong, Hebei and Jiangsu Provinces in China were frequent, which was also observed between the groups of China, Brazil, South Korea. Recombination, selection pressure and gene flow promote the evolution of the SPLCV in China.