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

Grapevine leafroll-associated virus-1 (GLRaV-1), one of the causal agents of Grapevine leafroll disease (GLRD), is oneof the most important viral diseases of grapevine worldwide. In this study, the prevalence of GLRaV-1, genetic variationand recombination events among GLRaV-1 isolates in Turkey were investigated. Initially, 197 grapevine samples fromdifferent provinces of the country were serologically tested. Of the total samples, 109 (55.32%) were identified asGLRaV-1 infected. Subsequently, 9 samples representing different geographic distribution were selected for furthersequence analysis of the heat-shock protein 70 homolog (HSP70h), open reading frame 9 (p24), coat protein (CP) andcoat protein duplicate 2 (CPd2). Among the four gene regions, CPd2 was found the most divergent region while HSP70hgene exhibited the lowest genetic diversity. The phylogenetic analysis of four genomic regions including GenBankrecords clustered all variants in two major groups and grouped Turkish isolates mostly together. However, the isolateclusters were not correlated to their geographic origin. Furthermore, several putative recombination events were detectedwith trace to moderate evidence support of algorithms implemented in Recombination Detection Program (RDP). Takentogether, the results provide a better understanding on genetic variation of Turkish GLRaV-1 isolates in the country andworldwide and can help to improve sanitation of propagated material programs for the grape growers.

PDF

___

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: 97-104
Alabi O, Rwahnih J, Karthikeyan M A, Poojari G, Fuchs S, Rowhani M & Naidu A (2011). Grapevine leafrollassociated 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. The Journal of Turkish Phytopathology 26: 121-129
Çığsar I, Digiaro M & Martelli G P (2002). Sanitary status of grapevines in south-eastern and central Anatolia (Turkey). Bulletin EPPO 32: 471-475
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
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 antibodybased 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 leafrollassociated virus 1 from China. Archives of Virology 160: 1669-1678
FAOSTAT (2014). FAOSTAT. Food and agriculture organization of the united nations. Retrieved in April 2016 from http://faostat.fao.org/default.aspx
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 leafrollassociated 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 (2014). Directory of virus and virus-like diseases of the grapevine and their agents. Journal of Plant Pathology 96: 105-120
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, Murrell B, Golden M, Khoosal A & Muhire B (2015). RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution 1(1): vev003
Önder S (2016). Ege Bölgesi bağlarında asma yaprak kıvrılma hastalığı ile ilişkili virüslerin tanılanması ve karakterizasyonu/Detection and characterization of grapevine leafroll-associated viruses (GLRaVs) in Aegean vineyards. PhD Thesis, Ege University, TR
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, Stecher G, Peterson D, Filipski A & Kumar S (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.