Abstract:The complete genome of a Cucumber green mottle mosaic virus isolate collected from watermelon in Ji’nan (CGMMV-JN) was amplified by RT-PCR. Sequencing analysis revealed that the full-length genome of CGMMV-JN is 6 424 nucleotides (nt) in length, of which the 5′-untranslated region (UTR) and 3′-UTR were 60 and 176 nt, respectively. The complete genome of CGMMV-JN contained four open reading frames (ORFs), which encode 129 kDa and 186 kDa RNA-dependent RNA polymerase (RdRp), 29 kDa movement protein, 17.4 kDa coat protein (CP), respectively. CGMMV-JN shared nucleotide identities of 90.0%-99.7% with other CGMMV isolates at the complete genome levels. Recombination analysis indicated that four isolates from Korea, Israel, India and China, respectively, presented recombination in ORF encoding RdRp. Phylogenetic tree analysis with complete genomic sequences demonstrated that the CGMMV isolates were clustered into three groups correlated with their geographical origin. Selection pressure analysis suggested that only CP ORF was under positive selection. Our study provided theoretical basis for the monitor and control of CGMMV.