Molecular variability and genetic structure of the population of Onion yellow dwarf virus infecting garlic in Iran

Baghalian, Kambiz; Kim, O. K.; Natzuaki, K. T.

doi:10.1007/s11262-010-0514-3

Cited by 9 publications

(7 citation statements)

References 20 publications

(29 reference statements)

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“…Phylogenetic analysis based on nucleotide sequences of CP gene of OYDV showed that geographical origin is not a demarcation criterion for grouping isolates (Baghalian et al. ). In line with this, the constructed phylogenetic tree (Fig.…”

Section: Discussionmentioning

confidence: 99%

Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in Sudan

Mohammed

Zicca²,

Manglli

et al. 2013

Journal of Phytopathology

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Allium sativum L. samples of three cultivars grown in Sudan were shown to contain several of the common garlic viruses of the genera Potyvirus, Carlavirus and Allexivirus. In particular, Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Garlic common latent virus (GarCLV), Garlic virus A (GVA), Garlic virus B (GVB), Garlic virus C (GVC) and Garlic virus X (GVX) were detected by reverse transcription polymerase chain reaction (RT-PCR) assay using degenerate genus-specific and virus-specific primer sets. Multiple viral infections with members of all three genera were found in all but one sample. Further, molecular and phylogenetic analysis of nucleotide and deduced amino acid sequences revealed that Sudanese isolates of LYSV, GarCLV and of Allexivirus genus were significantly divergent in partial coat protein genomic region from isolates of the same species retrieved from GenBank. This is the first report and study on viruses infecting garlic in Sudan.

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Section: Discussionmentioning

confidence: 99%

Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in Sudan

Mohammed

Zicca²,

Manglli

et al. 2013

Journal of Phytopathology

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“…Scallion mosaic virus (ScaMV, AJ310208), wild onion symptomless virus (WoSV) (LC159495), narcissus yellow stripe virus (NYSV, KU516386), and shallot yellow stripe virus (SYSV, AM267479) related to OYDV were used as outgroup for construction of rooted phylogenetic tree (Adams et al 2005). Low similarity rates obtained for LYSV and OYDV isolates were also obtained in studies on OYDV from Iran and LYSV from India (Baghalian et al 2010;Gupta et al 2017). In this context, findings reported from other studies support the results of the present study (Takaki et al 2005).…”

Section: Discussionmentioning

confidence: 69%

“…Furthermore, Alliaceae plants are frequently reported to be infected with carlavirus, allexivirus, and phytoplasma infections in addition to potyvirus infections (Wylie et al 2012;Abraham et al 2019). In particular, the fact that the virus entities in question cannot be identified in any of the collected onion samples supports the idea that the observed symptoms may be caused by infections of other viruses and virus-like diseases (Baghalian et al 2010;Gupta et al 2017).…”

Section: Discussionmentioning

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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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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“…In India, OYDVoccurs in epiphytotic proportion (Ahlawat and Varma 1997) and the highest incidence of OYDV infection was reported from Maharashtra, Gujarat and Madhya Pradesh (Gawande et al 2013). It has also been reported from several countries, including Argentina, Turkey, Iran, Serbia, Poland, Italy, Nepal, Sudan, Greece, Egypt, Brazil, Czech Republic and in the USA (Sevik and Akcura 2013;Baghalian et al 2010;Bagi et al 2012;Chodorska et al 2014;Manglli et al 2014;Majumder and Johari 2014 ). Here, we present the complete genome sequence of the OYDV isolate RR1 from onion (Allium cepa) in India.…”

Section: Introductionmentioning

confidence: 68%

Molecular characterization and recombination analysis of an Indian isolate of Onion yellow dwarf virus

et al. 2015

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This study presents the first whole genome sequence of Onion yellow dwarf virus (OYDV isolate RR1) from onion (Allium cepa) in India along with phylogenetic and recombination studies. We examined the sequence variability, distribution of simple sequence repeats (SSRs), and recombination breakpoints of different OYDV geographical isolates. The P1 and P3 regions of OYDV show a higher rate of sequence variability in amino acid and nucleotide sequences than other genomic regions. Entropy peaks of deduced amino acid sequences were higher in both regions (P1 and P3) of different OYDVs. The observed frequency of microsatellites was also higher in the P3 region of all OYDV genomes. The Indian isolate RR1 showed 75-98 % similarity with the other OYDV isolates in nucleotide and amino acid sequences and has 43 microsatellites and two compound microsatellites. It was most closely related to garlic isolate MS/SW1 from Australia. Isolate RR1 contained six recombination breakpoints in different genomic regions with the major parent related to the MS/SW1 (Australian) and SG1 (Spanish) OYDV isolates. The phylogenetic and recombination study demonstrated the divergence of Indian isolate RR1 from OYDV isolate from Australia.

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Molecular variability and genetic structure of the population of Onion yellow dwarf virus infecting garlic in Iran

Cited by 9 publications

References 20 publications

Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in Sudan

Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in Sudan

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

Molecular characterization and recombination analysis of an Indian isolate of Onion yellow dwarf virus

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