Molecular Characterization of Partial RdRp Genes of Tomato Ringspot Virus Isolates from Turkey

Year 2021, Issue: 21, 74 - 82, 31.01.2021

Nevin Akdura Murat Şevik

https://doi.org/10.31590/ejosat.813438

Abstract

Tomato ringspot virus (ToRSV) is a virus having isometric structure and single helix positive sense and is formed by a combination of two genomic RNA (RNA-1 and RNA-2) in the Secoviridae family from the Nepovirus group, and it causes economically devastating diseases in a wide range of hosts. In this study, 300 leaf samples from tomato (Solanum lycopersicum), pepper (Capsicum annuum), cucumber (Cucumis sativus) and grapevine (Vitis vinifera) plants exhibiting virus-like symptoms were collected from three different districts of Hakkari province between September 2014 and July 2015. The samples were tested for ToRSV infection on DNA fragments of 411 bp in size by Reverse Transcription Polymerase Chain Reaction (RT-PCR), using specific primers for the RNA dependent RNA polymerase (RdRp) gene. Seven out of 300 leaf samples (2.3%) were found to be infected with ToRSV. The virus was detected in tomato, pepper and cucumber samples, but its presence was not so evident in grapevine plants. The DNA sequences were submitted to GenBank (Accession numbers; KT728407, KT728408, KT728409 and KT728410). Our ToRSV isolates were compared with the ones available in GenBank, and the analysis of four ToRSV isolate RdRp gene sequences revealed that the nucleotide and amino acid homology were 83-100% and 94‐100%, respectively. Phylogenetic analysis suggested that Turkish ToRSV isolates and currently available ToRSV isolates in GenBank were divided into three distinct groups. This analysis provides, to the best of our knowledge, the first report on the partial RdRp sequence of ToRSV in Turkey.

Keywords

Tomato ringspot virus, Partial RNA dependent RNA polymerase gene, Reverse Transcription Polymerase Chain Reaction (RT-PCR), Sequence analysis

Supporting Institution

Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (TUBİTAK)

Project Number

TOVAG-114O864

Thanks

The study was supported by a grant from The Scientific and Technical Research Council of Turkey, TUBITAK (Project no: TOVAG-114O864). We are grateful to Dr. Stephan Winter, Dr. Wulf Menzel (Leibniz Institute DSMZ, German) and Farshad Rakhshandehroo (Islamic Azad University, Tehran, Iran) for providing us ToRSV isolate as positive control and support.

Türkiye'den Domates Halkalı Leke Virüsü İzolatlarının Kısmi RdRp Genlerinin Moleküler Karakterizasyonu

Abstract

Domates halkalı leke virüsü (ToRSV); Nepovirüs grubundan Secoviridae familyasında yer alan, iki genomik RNA (RNA-1 ve RNA-2) kombinasyonu ile oluşan izometrik yapıda ve tek sarmal pozitif duyarlı bir virüs olup, çeşitli konukçularda ekonomik olarak yıkıcı etkilere neden olmaktadır. Bu çalışmada, Eylül 2014 - Temmuz 2015 tarihleri arasında Hakkari ilinin üç farklı ilçesinden virüs benzeri belirtiler gösteren domates (Lycopersicon esculentum), biber Capsicum annuum), hıyar (Cucumis sativus) ve asma (Vitis vinifera) bitkilerinden 300 yaprak örneği toplanmıştır. Örnekler, RNA'ya bağlı RNA polimeraz (RdRp) geni için spesifik primerler kullanılarak Ters Transkripsiyon Polimeraz Zincir Reaksiyonu (RT-PCR) ile 411 bp boyutundaki DNA fragmanlarında ToRSV enfeksiyonu için test edilmiştir. 300 yaprak örneğinden yedisinin (% 2.3) ToRSV ile enfekte olduğu tespit edilmiştir. ToRSV, domates, biber ve hıyar örneklerinde tespit edilirken asma örneklerinde tespit edilmemiştir. Bu çalışma sonucunda elde edilen DNA dizileri GenBank'a yüklenmiştir (Erişim numaraları; KT728407, KT728408, KT728409 ve KT728410). Ülkemiz ToRSV izolatları GenBank'ta bulunan ToRSV izolatları ile karşılaştırılmış ve dört ToRSV izolatı RdRp gen sekansının analizi ile nükleotid ve amino asit benzerliğinin sırasıyla% 83-100 ve% 94-100 olduğu tespit edilmiştir. Filogenetik analiz, ülkemiz ve GenBank'ta mevcut bulunan ToRSV izolatlarının üç farklı gruba ayrıldığını göstermiştir. Yapılan bu çalışma, bilgimiz dahilinde, Türkiye'deki ToRSV'nin kısmi RdRp dizisinin ilk raporudur.

Keywords

Domates halkalı leke virüsü, Kısmi RNA bağımlı RNA polimeraz geni, Ters Kripsiyon Polimeraz Zincir Reaksiyonu (RT-PCR), Dizi analizi

Project Number

TOVAG-114O864

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