Genetic diversity and evidence of recombination in the coat protein gene of Onion yellow dwarf virus

Bereda, Maria; Paduch-Cichal, E.; Kalinowska, E.; Szyndel, Marek S.

doi:10.1007/s10658-015-0603-1

Cited by 2 publications

(2 citation statements)

References 21 publications

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“…In this context, it has been determined that isolates obtained from various continents, countries, and regions can be found in the same groups. Similar results have been reported in many studies on LYSV and OYDV isolates (Bereda et al 2015;Gupta et al 2017).…”

Section: Discussionsupporting

confidence: 91%

“…In many worldwide studies, LYSV and OYDV infections have been reported from different countries, and detailed analyses have been conducted concerning their genetic diversity (Dovas et al 2001;Fajardo et al 2001;Bereda et al 2015). However, the number of studies from Turkey that have investigated potyvirus infection in plants of the Allium genus is limited, and these studies have focused on identifying only LYSV and OYDV infections (Korkmaz and Cevik 2009;Fidan and Baloglu 2009;Santosa and Ertunc 2020).…”

Section: Introductionmentioning

confidence: 99%

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Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

Tuzlali¹,

Karanfil

Korkmaz

2021

3 Biotech

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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 doubleantibody 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.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

Tuzlali¹,

Karanfil

Korkmaz

2021

3 Biotech

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POPULATION GENETICS ANALYSIS OF Garlic virus A, Garlic virus B, Garlic virus C AND Garlic virus X

Bereda¹,

Paduch-Cichal²

2019

asphc

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Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C) and Garlic virus X (GarV-X) are members of the genus Allexivirus in the family Alphaflexiviridae. In this study, we collected 10, 30, 10 and 14 isolates of GarV-A, GarV-B, GarV-C and GarV-X, respectively, from different parts of Poland. All sequences of coat protein (CP) and nucleic-acid binding protein (NABP) regions of Allexivirus isolates available in GenBank were also included in this study. The nucleotide and amino acid sequences identities within each population differed substantially depending on the region of the genome and virus species. The results of selection pressure analysis showed that populations of each Allexivirus underwent negative selection, but the extent of the negative selection varied. It was also concluded that the GarV-A and GarV-C populations underwent a decrease in population size or balancing selection, while the GarV-B and GarV-X populations underwent an increase in population size. It was concluded that both populations of GarV-X evolved independently in each respective area, in contrast to populations of GarV-A, GarV-B and GarV-C.

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Genetic diversity and evidence of recombination in the coat protein gene of Onion yellow dwarf virus

Cited by 2 publications

References 21 publications

Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

Occurrence of leek yellow stripe virus and onion yellow dwarf virus from edible Allium plants in the south Marmara region of Turkey

POPULATION GENETICS ANALYSIS OF Garlic virus A, Garlic virus B, Garlic virus C AND Garlic virus X

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