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

Verma, Rakesh Kumar; Mishra, Ritesh; Petrov, N.; Stoyanova, Mariya; Stoev, A.; Bakardjieva, N.; Gaur, Rajarshi Kumar

doi:10.1007/s10658-015-0695-7

Cited by 15 publications

(5 citation statements)

References 33 publications

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“…Incidence of mixed infections with different begomoviruses and satellite molecules as well as the emergence of the new variants of viruses due to recombination of existing ones ( Fiallo-Olivé et al, 2019 ), has manifested the adaptability to new hosts, which has posed such a serious threat to many economically important crops ( Varma and Malathi, 2003 ). Recombination is a vital evolutionary approach for viruses ( Pagán and García-Arenal, 2018 ; Zaffalon et al, 2012 ) to get adapted to new environmental conditions ( Verma et al, 2015 ) concomitantly, it is the major driving force in the evolution of many viruses and also has been adequately revealed for ssDNA viruses especially begomoviruses ( Martin et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India

et al. 2020

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Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and subtropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10 −4 substitutions site −1 year −1), CLCuMuV (1.49 × 10 −4 substitutions site −1 year −1), ToLCGV (7.47 × 10 −4 substitutions site −1 year −1), the genome of associated ChiLCB (4.20 × 10 −4 substitutions site −1 year −1) and CLCuMuA (1.49 × 10 −4 substitutions site −1 year −1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.

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Section: Introductionmentioning

confidence: 99%

Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India

et al. 2020

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“…High sequence homology was also reported between OYDV isolates from India and those from Australia, i.e. 98% (Verma et al 2015). Similarly, Baghalian et al (2010) reported that among OYDV isolates from Iran shared 79 to 99% homology of the nucleotide sequence of coat protein gene, while with OYDV isolates from other countries Iran isolates shared 79 to 98% identity.…”

Section: Amplification Of Oydv and Sequence Analysismentioning

confidence: 74%

Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia

et al. 2020

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Abstract. Harti H, Hidayat SH, Sobir, Wiyono S. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas 21: 1697-1701. Research was conducted to identify main viruses infecting shallot in several regions in Indonesia and to further characterize genetic variation of Onion yellow dwarf virus (OYDV). Field survey was conducted in Central Java (Brebes), East Java (Probolinggo), West Sumatera (Alahan Panjang), West Nusa Tenggara (Bima), and South Sulawesi (Enrekang). Virus detection from field samples was conducted by dot immunobinding assay. This detection confirmed that infection of OYDV, Shallot yellow stunt virus (SYSV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) has occurred in all field with incidence ranged from 20 to 93.5%, 2 to 93%, 21.5 to 80%, and 2 to 80.5%, respectively. The specific primers of Nib gene successfully amplified DNA fragments of OYDV from all locations. Sequencing of DNA fragments revealed that the amplified product was 351 bp. Sequence analysis indicated that the present OYDV isolates from Indonesia shared homology from 82 to 95%; and they had homology from 81 to 95% with OYDV isolates from other countries. The similarity of OYDV isolates from different geographical locations reflected the movements of seed bulbs among and within countries. The phylogenetic tree also revealed that OYDV isolates from different countries did not group together indicating their diverse origin.

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“…Onion and garlic are affected with more than 20 notorious viruses of different genera including Allexivirus, Potyvirus, Tospovirus and Carlavirus are detected worldwide (Verma et al, 2015;Mansouri et al, 2021a). Symptoms produced by these viruses are identical to various other diseases and abiotic stresses, so difficult to identify based on symptoms only.…”

Section: Discussionmentioning

confidence: 99%

Current status and distribution of major RNA viruses infecting onion and garlic crops in Punjab, Pakistan

Hamza,

Ashfaq,

Riaz

et al. 2023

Emir J Food Agric

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Onion (Allium cepa L.) and garlic (Allium sativum L.) are significant bulbous vegetables well known for their kitchen and medicinal values across the globe including Pakistan. Allium crops are highly vulnerable to many notorious RNA viruses fit in different genera viz., Allexivirus, Potyvirus, Tospovirus and Carlavirus. These viruses are known to inflict colossal and havoc yield losses up to 50% in allium crops wherever they grown. The occurrence of allium viruses in Pakistan has already been reported, but in single crop and only a few studies describe their incidence and distribution. The study examined the current scenario and distribution of major RNA viruses infecting Allium crops in Punjab, Pakistan. Field surveys were carried out in 14 districts of Punjab province as well as capital territory Islamabad of Pakistan, for two consecutive growing seasons (2019 and 2020). The 3000 leaf samples collected, 1675 samples (Onion 791, Garlic 884) were found positive for RNA viruses by using specie specific DAS-ELISA and further confirmed through reverse transcriptase polymerase chain reaction (RT-PCR). The results revealed the presence of RNA viruses with overall disease incidence of 52.7% and the highest disease incidence was observed as Onion yellow dwarf virus (OYDV) 58% following Irish yellow spot virus (IYSV) 41.8% respectively in onion crop during 2019-2020. Similarly, in garlic crop overall disease incidence of RNA viruses was noticed as 58.9% and the highest disease incidence of OYDV was observed as 45%, following IYSV 32.4% and GarV-C 22.5% respectively during 2019-2020. Comparatively, disease incidence and geographical distribution of viruses was variable in surveyed regions of both crops during surveyed period, whereas OYDV and IYSV were most prevalent viruses infecting onion and garlic crops and GarV-C found only in garlic. The current study also concluded the importance to disseminate the information/awareness among the farmers regarding viral diseases and their management by using different strategies including use of resistant genotypes. Keywords: Allium crops; RNA viruses; ELISA; RT-PCR; Disease incidence; Virus distribution

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

Cited by 15 publications

References 33 publications

Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India

Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India

Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia

Current status and distribution of major RNA viruses infecting onion and garlic crops in Punjab, Pakistan

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