Molecular characterization of a new begomovirus infecting honeysuckle in Kobe, Japan

A virus (HY12) isolated from honeysuckle (Lonicera japonica Thunb.) collected in Kobe, Hyogo prefecture, Japan, showing symptoms of yellow vein mosaic, was characterized. HY12 was transmitted to Nicotiana benthamiana by sap inoculation while the other honeysuckle isolates could not. The complete DNA-A and DNA-β like molecules of the isolate were determined and found to comprise 2763 and 1262 nucleotides (nt), respectively, with a typical begomovirus genome organization. The DNA β molecule had the conserved ORF (β Cl) and satellite conserved region (SCR) typical of the Geminiviridae family containing a 5′-TAATATTAC-3′ motif in the stem loop and the adenine-(A) rich region. Additionally, its entire sequence was interrupted at intervals with sequences that were not viral and whose origin was unknown. A comparison of the DNA-A sequences revealed that HY12 shared 74% with four other honeysuckle begomoviruses but 88-89% with tobacco begomoviruses found in Japan. The isolate shared up to 92% of the IR sequences with the honeysuckle begomoviruses but only 60-88% with those of tobacco. Phylogenetic analysis of full length DNA-A component as well as its CP clustered HY12 with the tobacco begomoviruses. HY12 is an isolate of Honeysuckle yellow vein mosaic virus.