Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey

Morca, Ali Ferhan; Çeli̇k, Ali; Coşkan, Sevgi; Santosa, Adyatma Irawan; Akbaş, Birol

doi:10.1016/j.pmpp.2022.101786

Cited by 8 publications

(3 citation statements)

References 37 publications

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“…The appearance of spots on fruits ( Figure 1 ) seems to be due to discolouration only, different than those caused by tomato spotted wilt virus (TSWV, genus Orthotospovirus ), which mostly have dark halos around the discoloured areas. In addition to that, TSWV infections usually do not lead to severe blisters on fruits [ 37 ]. Tomato and pepper plants in greenhouses where ToBRFV was found were promptly eradicated and the greenhouses and tools were thoroughly sterilised using disinfectant.…”

Section: Discussionmentioning

confidence: 99%

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Çeli̇k

Coşkan²,

Morca³

et al. 2022

Plants

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A total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020–2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ω value range of 0.0869–0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low FST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV.

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Section: Discussionmentioning

confidence: 99%

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Çeli̇k

Coşkan²,

Morca³

et al. 2022

Plants

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“…The DAS-ELISA method is widely used in the studies conducted in tomato and pepper production areas (Arli-Sokmen et al, 2005;Arli-Sokmen & Sevik, 2006;Yardımcı & Eryiğit, 2006). During 2019-2020, leaf samples were collected, and RT-PCR tests confirmed TSWV infection in tomato and pepper from various provinces from Turkey except for İzmir (Beşkeçili et al, 2021;Morca et al, 2022). Currently, İzmir province has an important position in terms of tomato and pepper production and exportation (TUİK, 2022).…”

Section: Introductionmentioning

confidence: 99%

İzmir ilinde domates ve biber bitkilerini etkileyen tomato spotted wilt virus (TSWV) ve cucumber mosaic virus (CMV) etmenlerinin moleküler karakterizasyonu

Güneş

Paylan²,

Gümüş³

2023

Ege Üniversitesi Ziraat Fakültesi Dergisi

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Objective: The objective of this study was to investigate tomato spotted wilt virus (TSWV) and cucumber mosaic virus (CMV) infections in tomato and pepper plants showing virus-induced symptoms in vegetable growing districts of İzmir, Turkey. Material and Methods: Surveys were carried out in tomato and pepper plantations in 2019 and 2021, and the incidences of these viruses in the collected leaf samples were determined by RT-PCR. Nucleotide identities and phylogenetic relationships of the TSWV and CMV isolates with other isolates retrieved from the GenBank database were determined. Results: The results of this study showed that tomato plants were infected at the same rate (21.50%) with TSWV and CMV. Out of the tested pepper samples, 64.15% were infected with TSWV and 25.47% with CMV. The results showed that, the identity rate of nucleoprotein region of TSWV isolates from tomato was 99-96% at nucleotide level while the isolates from pepper showed 100-95% identity. On the other hand, the capsid protein gene region of the tomato isolate of CMV had nucleotide identity rate of 98-95% with other isolates in GenBank, while that of its pepper isolates had 100-98% identity. Also, CMV isolates of this study showed close phylogenetic relationship with the CMV isolates of subgroup IB. Conclusion: This study revealed the prevalence of TSWV and CMV in symptomatic tomato and pepper samples in İzmir province and some molecular properties of them.

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“…Recombination and reassortment are the most frequently found evolutionary forces in populations of both RNA and DNA plant viruses, thus significantly affecting their genetic variation (Chare and Holmes, 2006;Gibbs et al, 2008). While population genetics of many emerging plant RNA viruses have been discussed in recent papers (Randa-Zelyüt and Ertunç, 2021;Tokhmechi et al, 2021;Morca et al, 2022), the genetic variability and evolutionary mechanisms of populations of DNA viruses were remained less studied (Sanz et al, 1999;Ng et al, 2011). Citrus spp., themselves, as commercially important fruits in Turkey, are constantly improved through breeding (Kurtuluş et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

First Insight into Genetic Variation and Population Structure of The Emerging Citrus chlorotic dwarf-associated virus (CCDaV, genus Citlodavirus)

ZELYÜT

SANTOSA

Karanfil

et al. 2022

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi

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Citrus spp. is widely planted in tropical and subtropical regions, including in Turkey and other Mediterranean countries. Due to its widespread vector and climate change, Citrus chlorotic dwarf-associated virus (CCDaV), a member of the newly formed genus Citlodavirus, is one of the emerging viruses that can be a serious constraint to Citrus crops production in the coming years. Therefore, in-silico analysis on all available isolates in NCBI GenBank was performed to provide the first insight into the genetic population and evolution of CCDaV, which may contribute to its control. CCDaV phylogroups based on full genome, complete movement protein, and complete coat protein sequences were found to be not associated with isolate origins or host species, and all isolates also shared a high genetic identity among them. However, neutrality tests indicated that the current populations are expanding, driven by new mutations. Low Fixation index (FST) values (0.00000-0.36207) confirmed no genetic separation among different ORFs of isolates from three countries. The constructed TimeTree suggested that CCDaV emergence was very recent compared to the other three members of the genus Citlodavirus. Therefore, the obtained results of this study could also expand our knowledge on other even more obscure citladovirus and even other plant DNA viruses, which are still less studied than RNA viruses.

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Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey

Cited by 8 publications

References 37 publications

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

İzmir ilinde domates ve biber bitkilerini etkileyen tomato spotted wilt virus (TSWV) ve cucumber mosaic virus (CMV) etmenlerinin moleküler karakterizasyonu

First Insight into Genetic Variation and Population Structure of The Emerging Citrus chlorotic dwarf-associated virus (CCDaV, genus Citlodavirus)

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