Abstract
Among edible Allium plants (leek, onion, and garlic), leek yellow stripe (LYSV) and onion yellow dwarf virus (OYDV) are the most common viruses worldwide. While the presence of these two viruses in Turkey has previously been confirmed, only a few studies on their prevalence and genetic diversity have been performed. The aim of this study, conducted in the southern Marmara region of Turkey (SMR), was to identify the presence and genetic diversity of these viruses. Samples were collected from 494 plants exhibiting virus and virus-like symptoms. Samples were tested for the relevant viruses by double-antibody sandwich enzyme-linked immunosorbent assay and reverse transcription polymerase chain reaction (DAS-ELISA and RT-PCR, respectively). Tests revealed the presence of OYDV in 95 samples and LYSV in 52, whereas 33 samples were observed to have a combined infection. To examine the genetic diversity, 10 isolates from each virus were chosen from the infected samples. Using RT-PCR, the complete coat protein (CP) gene for LYSV and a partial sequence region of the nuclear inclusion b + CP gene for OYDV were amplified, cloned, and sequenced from the selected isolates. The sequence data were compared with the isolates in GenBank; it was determined that SMR LYSV and OYDV isolates show similarities over 77% with world isolates at the nucleotide and amino acid levels. Phylogenetic analyses showed that the LYSV and OYDV isolates had some diversity with isolates from different parts of the world, and the host had an important role in the phylogenetic relationships, particularly for LYSV. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03067-1.