Characteristics of the genome of ageratum yellow vein China virus infecting Sonchus oleraceus

Sonchus ( ) was originated from Europe and now is cultivated worldwide. The wild resources of sonchus are very abundant, it has rich nutritional value and medicinal value. In this study, 15 sonchus samples with typical symptoms showing leaf curling, vein thickening, enation et al., were collected from Guigang and Baise city of Guangxi, China. Viruses in the diseased sonchus were identified, and their genomes were analyzed for phylogenetic relationship and for recombination. The results showed that all the samples were confirmed to be infected with begomoviruses, and 3 full-length genome were obtained from 15 sonchus, named GG7-13, GG8-6, and BS63-5, and the genome lengths were 2584 nt, 2735 nt, and 2746 nt, respectively. The nucleotide identities among the three isolates were 92.67 - 99.93%. All of them shared the highest identities (greater than 91.69%) with other isolates of ageratum yellow vein China virus (AYVCNV) available on GenBank. According to the guidelines of classification of begomoviruses, they are different isolates of AYVCNV; phylogenetic tree analysis showed that these isolates were formed a large branch with 3 other Guangxi isolates of AYVCNV, indicating their close evolution. The genome structures of GG8-6 and BS63-5 are consistent with the monopartite genome virus of the begomoviruses, and both have 6 ORFs, while GG7-13 has a 151 nt deletion between C2 and C3, resulting in a mutant strain of only 5 ORFs. This study is the first report on Sonchus oleraceus infected by ageratum yellow vein China virus.