Abstract: To investigate whether pumpkins displaying mosaic symptoms harbor plant viruses, we conducted an analysis of pumpkin samples from Sichuan using the small-RNA deep sequencing technique. We analyzed a complete genome of the zucchini yellow mosaic virus (ZYMV), designated as the SCSN isolate. The SCSN isolate has a genome length of 9572 nt and encodes a 351.1 kDa polyprotein. Comparative sequence analysis revealed that the SCSN isolate shares the highest similarity (97.4% amino acid identity) with the WM isolated from Zhejiang. Recombination analysis indicated that the SCSN isolate originated from recombination events involving the WM isolate and the Ver isolate from Spain. A phylogenetic analysis, based on the SCSN whole genome sequence and 159 sequences from GenBank with a genome length exceeding 9300 nt, revealed clustering of ZYMV isolates from 28 countries and regions into seven distinct groups. Notably, the SCSN isolates formed a distinct cluster within the first group. There was a correlation between the phylogenetic evolution of ZYMV and its geographical distribution, highlighting the existence of dominant ZYMV taxa. As far as this knowledge, this is the first report of the complete genome of a ZYMV isolated from Sichuan, and would contribute to the development of strategies for preventing the spread of ZYMV through long-distance transmission.

Key words: zucchini yellow mosaic virus, isolate, complete genome, recombination, phyletic evolution, pumpkin