Phylogenetic study of iris yellow spot tospovirus (IYSV) isolates from Italy based on nucleocapsid (N) gene

Iris yellow spot tospovirus (IYSV), member of the genus Orthotospovirus, family Tospoviridae, is present in most allium growing regions in the world and its host range includes cultivated and wild onions, garlic, chives, leeks and several ornamentals (Gent et al., 2006; Turina et al., 2012). In previous phylogenetic studies, two main sub-groups were identified on the basis of nucleocapsid gene (N), American and Eurasian (Bag et al., 2015) and based on RFLP, two genotypes, NL and BR (Iftikhar et al., 2014). During a three-year survey carried out in Calabria (southern Italy), IYSV was detected for the first time in a large onion production area where cv Rossa di Tropea is widely cultivated. To better understand the population dynamics, and correlation to their geographic, host and/or temporal factors, a new IYSV phylogenetic study based on complete N gene sequences was carried out. Ten Calabrian IYSV isolates, and three from other regions of Italy, Campania, Marche and Veneto, were analyzed including a large number of IYSV N gene sequences retrieved in GenBank, for a total of about 170 isolates worldwide, reported from Allium spp. and ornamentals. Phylogenetic rooted trees were generated using Neighbor Joining (NJ) method (Tamura 3-parameter model with 2000 bootstrap replicates) available in MEGA 6. Phylogenetic analysis confirmed the main dichotomic tree topology consisting of American and Eurasian clades. Interestingly, the Americas clade had isolates from Allium cepa L., whereas the Eurasian group, with the exception of isolates from India, had IYSV sequences derived from ornamentals plants. IYSV isolates from Japan were in two clades (America and Eurasia) according to host, onion and ornamental alliaceae, respectively. Interestingly, in the Americas clade, a sub-clade, characterized by short branch demarcations, included all the Italian isolates along with those from Serbia, and Tajikistan. Findings from this new phylogenetic reconstruction, suggests different IYSV origin points or evolution with a clear separation, and provides basis for further evaluation of the population dynamics of IYSV.