Genetic diversity analyses of leek yellow stripe virus and onion yellow dwarf virus in Japan

The genus Allium is widely distributed throughout the world, and the cultivated Allium crop species, especially garlic (Allium sativum), are extensively consumed and traded both inter- and intra-countries. While several viruses are known to be associated with the distribution of Allium spp., two potyviruses classified leek yellow stripe virus (LYSV) and onion yellow dwarf virus (OYDV) are particularly considered as devastating pathogenic viruses with a widespread incidence. To understand the evolutionary characterization of the two potyviruses in Japan, authors analyzed the phylogenetic and genetic diversity based on their coat protein (CP) genes, which are the most conserved regions in the potyvirus genome. As a result of the phylogenetic analysis, LYSV and OYDV in Japan were largely divided into 4 and 5 groups, respectively. Among the 36 Japanese isolates of LYSV, most isolates were clustered based on the geographical factors where the isolates occurred: 18 isolates into the Northern group, 12 isolates into the Southern group, and 3 isolates into the Okinawa group.Furthermore, two isolates from leek (A. porrum) formed a distinct group along with an isolate from garlic, suggesting a possibility of LYSV cross-transmission between garlic and leek. The phylogenetic analysis of the 39 Japanese isolates of OYDV indicated that they were split into 5 distinct clusters without any geographical or natural host relationships. Among these, two groups consisting of 18 and 14 isolates were predominantly found in Japan, showing different identity ranges of 85.6 to 99.8% and 95.5 to 100%, respectively. In both species, recombinant intra-species and co-infection with distinct phylogenetic groups were observed, promoting their genetic diversification. Even though both potyviruses occurred in the same host range and country, they showed different evolutionary scenarios so far, and further studies are needed to understand virus evolution better.