Asma yaprak kıvırcıklık virüsü-1 Türk izolatlarının Genetik Varyasyon ve Rekombinasyon Analizleri

Year 2019, Volume: 25 Issue: 3, 319 - 327, 05.09.2019

Eminur Elçi

https://doi.org/10.15832/ankutbd.402162

Cited By: 3

Abstract

Asma yaprak
kıvırcıklık virüsü -1 (Grapevine leafroll-associated virus 1-GLRaV-1), asma yaprak kıvırcıklık hastalığına (Grapevine
leafroll disease-GLRD) neden olan etmenler arasında yer almakta olup dünya
çapında virüs kökenli bağ hastalıkları arasında önem derecesi yüksektir. Bu çalışmada,
Türkiye’den izole edilen GLRaV-1’ in yaygınlık derecesi, genetik varyasyonu ve
rekombinasyon olayları araştırılmıştır. İlk olarak, farklı bölgelerden toplanan
197 adet asma örneği serolojik olarak test edilmiştir. Test edilen örneklerden
109 adetinin (%55.32) GLRaV-1 ile infekte olduğu tespit edilmiştir. İnfekte
olduğu tespit edilen bu örnekler arasından her bir coğrafik bölgeyi temsil eden
9 adet izolat seçilerek GLRaV-1’in kılıf proteini (CP), ikincil kılıf proteini
(CPd2), açık okuma çerçevesi 9 (p24) ve ısı şok protein homologu 70 (HSP70h)
gen bölgelerinin genetik analizleri yapılmıştır. Yapılan analizlerde, çalışılan
dört gen bölgesinden CPd2 gen bölgesinin genetik çeşitliliğinin en yüksek
olduğu gözlenirken en korumalı bölgenin HSP70h geni olduğu tespit edilmiştir.
Gen Bankasından alınan kayıtların da kullanılması ile oluşturulan filogenetik
analizler sonucunda, izolatların iki büyük grup altında kümelendiği ve Türk
izolatlarının da çoğunlukla aynı grup içerisinnde kümelendiği tespit edilmiştir.
Fakat, değişik coğrafik bölgelerden toplanan izolatların coğrafik bölgeye göre kümelenmediği
tespit edilmiştir. Bununla birlikte, Rekombinasyon Bulma Programında (RDP) yer
alan algoritmaların aracılığı ile yapılan analizlerde çeşitli rekombinasyon
olayları gözlenmiştir. Sonuç olarak, elde edilen bu veriler GLRaV-1’in gerek
ülkesel gerekse dünya çapında genetik varyasyon çalışmalarına katkı sağlamakta
olup bağcılıkta üretim materyallerinin sanitasyon programlarının
geliştirilmesine yardımcı olacağı düşünülmektedir.

Keywords

Vitis vinifera L., CP, CPd2, p24, HSP70h, genetik varyasyon

Genomic Variability and Recombination Analysis of Grapevine leafroll-associated virus-1 Isolates from Turkey

Abstract

Grapevine leafroll-associated virus-1 (GLRaV-1), one of the causal agents of Grapevine leafroll disease (GLRD), is one of the most important viral diseases of grapevine worldwide. In this study, the prevalence of GLRaV-1, genetic variation and recombination events among GLRaV-1 isolates in Turkey were investigated. Initially, 197 grapevine samples from different provinces of the country were serologically tested. Of the total samples, 109 (55.32%) were identified as GLRaV-1 infected. Subsequently, 9 samples representing different geographic distribution were selected for further sequence analysis of the heat-shock protein 70 homolog (HSP70h), open reading frame 9 (p24), coat protein (CP) and coat protein duplicate 2 (CPd2). Among the four gene regions, CPd2 was found the most divergent region while HSP70h gene exhibited the lowest genetic diversity. The phylogenetic analysis of four genomic regions including GenBank records clustered all variants in two major groups and grouped Turkish isolates mostly together. However, the isolate clusters were not correlated to their geographic origin. Furthermore, several putative recombination events were detected with trace to moderate evidence support of algorithms implemented in Recombination Detection Program (RDP). Taken together, the results provide a better understanding on genetic variation of Turkish GLRaV-1 isolates in the country and worldwide and can help to improve sanitation of propagated material programs for the grape growers.

Keywords

Vitis vinifera L., CP, CPd2, p24, HSP70h, genetic variation

References

• Akbaş B, Kunter B & Ilhan D (2007). Occurrence and distribution of grapevine leafroll-associated viruses 1, 2, 3 and 7 in Turkey. Journal of Phytopathology 155: 122-124.
• Akbaş B, Kunter B & Ilhan D (2009). Influence of leafroll on local grapevine cultivars in agroecological conditions of central Anatolia region. Horticulture Science (Prague) 36: 97-1004.
• Alabi O, Rwahnih J, Karthikeyan M A, Poojari G, Fuchs S, Rowhani M & Naidu A (2011). Grapevine leafroll-associated virus 1 occurs as genetically diverse populations. Phytopathology 101: 1446–1456.
• Çağlayan K (1997). Incidence of grapevine leafroll, grapevine virus A and tomato black ring virus in the vineyards of Hatay province. Journal of Phytopathology 261: 21-128.
• Clark M F & Adams A N (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. Journal of General Virology 34: 475-483.
• Çığsar I, Digiaro M & Martelli G P (2002). Sanitary status of grapevines in south-eastern and central Anatolia (Turkey). Bulletin EPPO 32: 471-475.
• Cseh E, Takacs P A, Gáborjányi R, Palkovics L & Kocsis L (2013). RT-PCR analysis and evolutionary relationship of some Hungarian grapevine leafroll associated virus 1 and 3 isolates. American Journal of Plant Science 4: 2006-2010.
• Değer E, Gazel M & Çağlayan K (2015). Current status of grapevine leafroll associated viruses in Hatay and Gaziantep provinces in Turkey. In: Proceedings of the 18th Congress of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine (ICVG), 7-11 September, Ankara, Turkey, pp. 164-165.
• Dolja V K, Karasev K & Koonin E V (1994). Molecular biology and evolution of Closteroviruses: Sophisticated build-up of large RNA genomes. Annual Review of Phytopathology 32: 261-285.
• Esteves F, Teixeira Santos M, Eiras-Dias J E & Fonseca F (2013). Molecular data mining to improve antibody-based detection of grapevine leafroll-associated virus-1 (GLRaV-1). Journal of Virology Methods 194: 258–270.
• Fan X, Hong N, Dong Y, Ma Y, Zhang Z P, Ren F, Hu G, Zhou J & Wang G (2015). Genetic diversity and recombination analysis of grapevine leaf roll-associated virus 1 from China. Archives of Virology 160: 1669-1678.
• Fazeli C F & Rezaian M A (2000). Nucleotide sequence and organization of ten open reading frames in the genome of grapevine leafroll-associated virus 1 and identification of three subgenomic RNAs. Journal of General Virology 81(3): 605-615.
• Karasev A V (2000). Genetic diversity and evolution of closteroviruses. Annual Review of Phytopathology 38: 293-324.
• Kominek P, Glasa M & Bryxiová M (2005). Analysis of the molecular variability of grapevine leafroll-associated virus 1 reveals the presence of two distinct virus groups and their mixed occurrence in grapevines. Virus Genes 31: 247-255.
• Köklü G, Digiaro M & Savino V (1998). A survey of grapevine viruses in Turkish Thrace. Phytopathologia Mediterranea 37: 140-142.
• Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A & McWilliam (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23(21): 2947-2948.
• Little A, Fazeli C F & Rezaian M A (2001). Hypervariable genes in grapevine leafroll- associated virus 1. Virus Research 80: 109-116.
• Martelli G P, Agranovsky A A, Al Rwahnih M, Dolja V V, Dovas C I & Fuchs M (2012). Taxonomic revision of the family Closteroviridae with special reference to the grapevine leafroll-associated members of the genus Ampelovirus and the putative species unassigned to the family. Journal of Plant Pathology 94: 7–19.
• Martin D P, Lemey P, Lott M, Moultan V, Posada D & Lefeuvre P (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
• Özaslan M & Yilmaz M A (1985). Adana Tarsus Gaziantep Şanlıurfa ve Adıyaman bölgelerinde yetiştirilen bağlara zarar veren virüs hastalıkları. In: Proceedings of the VII. Türkiye Fitopatoloji Kongresi, 26-29 Eylül, Turkey, pp. 306-312.
• Predajna L, Gaziova A, Holovıčová E & Glasa M (2013). Analysis of a short genomic region of grapevine leafroll-associated virus 1 (GLRaV-1) reveals the presence of two different molecular groups of isolates in Slovakia. Acta Virology 57(3): 353-356.
• Sforza R, Boudon-Padieu E & Grei C (2003). New mealybug species vectoring grapevine leaf roll associated viruses-1 and -3 (GLRaV-1 and -3). European Journal of Plant Pathology 109: 975–981.
• Simon-Loriere E & Holmes E C (2011). Why do RNA viruses recombine?. Nature Reviews Microbiology 6: 617-626.
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology Evolution 28(10): 2731-2739.