Molecular analysis of the 3’ terminal region of Onion yellow dwarf virus from onion in southern Italy

Onion yellow dwarf virus (OYDV) is an economically important pathogen causing severe disease in garlic, onion and other Allium crops. Eleven isolates of OYDV, all from onion originating from Calabria, southern Italy, were genetically analyzed. An OYDV onion isolate from Sudan was also included in this study. The 3’ terminal region of about 2.5 kb of the twelve isolates were sequenced and the sequences comprising a part of the nuclear inclusion a (NIa-Pro), the complete nuclear inclusion b (NIb) and coat protein (CP) genes and the 3’ untranslated region (3’UTR), were compared to each other and to corresponding sequences of other OYDV isolates from different countries and Allium hosts. The within-population nucleotide identity of the Italian OYDV onion isolates was very high (more than 99.3%), whereas nucleotide identity between them and OYDV onion isolates from Germany was 94%, Argentina 92% and Sudan 87%. Recombination analysis among the complete 3’ terminal sequences showed putative recombination breakpoints in the NIb region of the Argentine isolate, with the minor parent related to the Sudanese isolate. Comparison between OYDV isolates from onion and isolates from garlic produced identities of 77-78% for the complete nucleotide region. When the 3’ terminal nucleotide sequence and the complete NIb protein were analyzed, the phylogenetic analysis generated rooted trees with high bootstrap values (100%), showing a genetic grouping into two well separated clades distinctive for onion and garlic isolates of OYDV. Phylogenetic analysis of CP protein and 3’UTR showed lower bootstrap separation values and no distinct sub-grouping of the OYDV isolates from the two major Allium species.