Identification and molecular characterization of a novel bipartite begomovirus infecting groundsel (Senecio scandens) in China

Begomoviruses (family Geminiviruses) are plant viruses with a worldwide distribution, cause severe viral diseases, and result in a reduction in crop production. In this study, a novel bipartite begomovirus tentatively named Groundsel yellow mosaic virus (GYMV) was characterized. The complete genome of GYMV was determined by RNA sequencing, back-to-back PCR, and rolling-circle amplification technologies, to contain 2,712 (DNA-A) and 2,658 (DNA-B) nucleotides. Six and two open reading frames were predicted in the DNA-A and DNA-B sequences, respectively. A stem-loop structure with the conserved nonanucleotide TAATATTAC was found in both DNA-A and DNA-B. GYMV showed important features of “Old World” begomoviruses, such as the small protein AC2/pre-coat coded in DNA-A virion-sense strand, and the putative “TATA-Box + ACTT-N7-AAGT” composite element in homologous CP promoter region. A pairwise identity analysis revealed that the GYMV genome shared less than a 74% identity with known geminiviruses. Recombination and phylogenetic analyses showed that GYMV did not arise from recombination, but is a new species of genus Begomovirus family Geminiviridae that could infect groundsel.