Bolu ilinde Plum pox virus’un belirlenmesi ve kısmi moleküler karakterizasyonu

Year 2020, Volume: 60 Issue: 4, 59 - 68, 31.12.2020

Ali Ferhan Morca , Sevgi Coşkan , Faruk Öncü

https://doi.org/10.16955/bitkorb.719732

Cited By: 5

Abstract

Plum pox virus (PPV), sert çekirdekli meyvelerde verim, kalite ve ekonomik kayıplara sebep olan Şarka hastalığının etmenidir. PPV, Avrupa başta olmak üzere dünya çapında tespit edilmiştir. Türkiye’de bugüne kadar yapılan çalışmalarda etmenin varlığı farklı bölgelerde sınırlı olarak tespit edilmiştir. Bolu ilinde şu ana kadar PPV’nin tespitine ilişkin herhangi bir kayıt bulunmamaktadır. Bolu ilinde 2016-2019 yılları arasında yapılan sürveyler neticesinde 306 örnek toplanmıştır. PPV’nin varlığını tespit etmek amacıyla ilk olarak DAS-ELISA ile örnekler analiz edilmiş, sadece üç adet şeftali örneğinin PPV ile enfekteli olduğu belirlenmiştir. Enfekteli örnekler daha sonra üniversal primerler (P1/P2) kullanılarak RT-PCR ile test edilmiş ve DAS-ELISA sonuçları doğrulanmıştır. Ayrıca PPV’nin ırka spesifik primerleri ile ırk düzeyinde de teşhisleri yapılmıştır. Irk düzeyinde yapılan bu teşhislerde örneklerin PPV-M (Marcus) ırkı ile enfekteli olduğu belirlenmiştir. Moleküler çalışmalar sonucunda üç izolatın kısmi kılıf protein bölgesine ait 243 nükleotidlik dizileri elde edilerek NCBI’a kaydedilmiştir. Ayrıca 38 temsili PPV sekans dizisi ile yapılan filogenetik analiz (Neighbour-Joining) sonucunda, BLAST analizinde olduğu gibi Bolu izolatlarının PPV-M izolatları ile kümelenerek diğer PPV ırklarından ayrıldığı görülmüştür. Yapılan bu çalışma ile elde edilen PPV izolatları Bolu ili için ilk kayıt niteliğindedir. Sonuç olarak, Bolu ilinde daha kapsamlı sürveylerin yapılması ve elde edilen izolatlarının tam genom dizileri elde edilerek genetik varyasyonlarının belirlenmesinin gerekliliği ortaya çıkmıştır. Enfekteli bulunan ağaçların ise tamamı imha edilmiştir.

Keywords

PPV, şarka, şeftali, M ırkı, filogenetik ağaç, sekans

Determination and partial molecular characterization of Plum pox virus in Bolu province

Abstract

Plum pox virus (PPV), the causal agent of Sharka disease, causes yield, quality, and economic losses in stone fruits. PPV has been reported worldwide, especially in Europe. In studies to date, the presence of the virus has been identified as being restricted in different regions of Turkey. However, there is no record of PPV in Bolu province so far. Hence, surveys were carried out in Bolu province between 2016-2019, and a total of 306 samples were collected. To determine the presence of PPV, the samples were first tested by DAS-ELISA, and only three peach samples were found to be infected. DAS-ELISA results of infected samples were confirmed by RT-PCR using universal primers (P1/P2), then infected samples were identified at the strain level using strain-specific primers. The samples were found to be infected with the PPV-M (Marcus) strain and 243-bp long nucleotide sequences containing the partial coat protein gene of three isolates were deposited to NCBI. Phylogenetic analysis (Neighbor-Joining) generated by 38 representative PPV sequences indicated that Bolu isolates were clustered with PPV-M isolates and separated from other strains, as in BLAST analysis. To our knowledge, this is the first report of PPV in Bolu. This study reveals the necessity to carry out more extensive surveys to prevent the PPV dissemination in Bolu and to identify the complete genomes of the obtained isolates to determine their genetic variation. All the PPV-infected trees were destroyed as a consequence.

Keywords

PPV, sharka, peach, M strain, phylogenetic tree, sequence, phylogenetic tree

References

• Akbaş B., Değirmenci K., Çiftçi O., Kaya A., Yurtmen M., Uzunoğulları N., Çelik N., Türkölmez Ş., 2011. Update on Plum pox virus distribution in Turkey, Phytopathologia Mediterranea, 50, 75−83.
• Atanassov D., 1932. “Plum pox A new virus disease”, Annals of the University of Sofía Faculty of Agriculture and Silviculture, 11: 49-69.
• Azeri T., 1994. Detection of Virus Diseases of Stone Fruits in Agean Region of Turkiye. 9th Congress of Mediterranean Phytopathological Union, Kuşadası, Aydın, Türkiye, 511-513.
• Brunt A.A., Crabtree K., Dallwitz M.J., Gibbs A.J., Watson L., Zurcher E.J., 1996. Plant viruses online: descriptions and lists from the VIDE database. Version: 16th January 1997. URL http://biology. anu. edu. au/Groups/MES/vide/refs. htm.
• Buzkan N., Öztekin V., Demir M., Onura D., Ilgın M., 2006. SEKAMER Kayısı Koleksiyon Parselindeki Ağaçlarda Virüs Hastalıklarının Saptanması ve Çözüm Yolları. KSÜ. Fen ve Mühendislik Dergisi; 9(2), 2006.
• Candresse T., Svanella-Dumas L., Gentit P., Çağlayan K., Çevik B., 2007. First report of the presence of Plum pox virus Rec strain in Turkey. Plant Disease 91(3):331
• Cambra M. A., Crespo J., Gorris M.T., Martínez M.C., Olmos A., Capote N., Cambra M., 2004. Detection and eradication of Plum pox virus Marcus type in Aragón (Spain). Acta horticulturae, 657, 231-235.
• Cambra M., Capote N., Myrta A,. Llácer G., 2006. Plum pox virus and the estimated costs associated with sharka disease. EPPO Bull. 36: 202–204.
• Cervera M.T., Riechmann J.L., Martín M.T., García J.A., 1993. 3′-terminal sequence of the plum pox virus PS and ǒ6 isolates: Evidence for RNA recombination within the potyvirus group. Journal of General Virology, 74(3), 329-334.
• Ceylan A., Gürcan K., Akbulut M., Ghaderi M., 2014. Kayseri’de yüksek şarka enfeksiyonu. Erciyes Üniversitesi Fen Bilimleri Enstitüsü Fen Bilimleri Dergisi, 30(2), 80-85.
• Chirkov S., Ivanov P., Sheveleva A., 2013. Detection and partial molecular characterization of atypical Plum pox virus isolates from naturally infected sour cherry. Archives of Virology, 158(6), 1383-1387.
• Chirkov S., Sheveleva A., Ivanov P., Zakubanskiy A., 2018. Analysis of genetic diversity of Russian sour cherry Plum pox virus isolates provides evidence of a new strain. Plant Disease 102(3), 569-575.
• 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(3), 475-483.
• Cui H., Wang A., 2016. Plum pox virus 6K1 protein is required for viral replication and targets the viral replication complex at the early stage of infection. J. Virol. 90 (10), 5119–5131. doi: 10.1128/JVI.00024-16.
• Çelik N., Kütük B.T., 2013. Antalya ilinde şarka virüs hastalığının belirlenmesi. Derim, 30(2), 1-10.
• Dallot S., Glasa M., Jevremovic D., Kamenova I., Paunovic S., Labonne G., 2011. Mediterranean and central-eastern European countries host viruses of two different clades of Plum pox virus strain M. Archive of Virology, 156 (3), 539–542.
• Değirmenci K., Morca A.F., Umar S., 2016. New Infection Areas of Plum pox virus (PPV) in Turkey. 3rd International Symposium on Plum pox virus, 9-13 May 2016 Antalya-Turkey. S:37.
• Deligöz İ., Değirmenci K., Sökmen M., 2015. Samsun İlinde Sert Çekirdekli Meyve Türlerinde Şarka Hastalığı Etmeninin (Plum pox virus) Belirlenmesi. Anadolu Tarım Bilimleri Dergisi, 30 (3), 227-235.
• Desvignes J.C., Boyé R., Cornaggia D., Grasseau N., Hurtt S., Waterworth H., 1999. Virus diseases of fruit trees. (Diseases due to viroids, viruses, phytoplasmas and other undetermined infectious agents). Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL).
• Dunez J., 1986. Preliminary observations on virus and virus like diseases of stone fruit trees in Mediterranean and near east countries. FAO Plant Protection Bulletin, 34: 43-48.
• Dzhuvinov V.T., Bozhkova V.B., Milusheva S.A., Gercheva P.S., 2007. Investigation of Plum Pox Virus in Bulgaria for the past 70 years. Bulgarian Journal of Agricultural Science, 13(3), 265.
• Elibuyuk İ.Ö., 2004. Current situation of sharka disease in Ankara, Turkey. Phytoparasitica, 32 (4), 417–420.
• Elibüyük İ.Ö., 2005. Ankara’da Şeftali Ağaçlarında Görülen Şarka Hastalığı Üzerinde Araştırmalar. Tarım Bilimleri dergisi, 11(3), 236-243.
• EPPO, 2020. https://gd.eppo.int/taxon/PPV000 Erişim tarihi: 30.03.2020
• Fernández-Calvino, L., López-Abella, D., López-Moya, J. J., & Fereres, A. (2006). Comparison of Potato Virus Y and Plum Pox Virus transmission by two aphid species in relation to their probing behavior. Phytoparasitica, 34(3), 315.
• Foissac X., Svanella-Dumas L., Dulucq M.J., Candresse T., Gentit P., Clark M.F., 2001. Polyvelent detection of fruit tree tricho, capillo and foveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR). Acta Horticulturae 550:37-43.
• Gazel M., Serce C.U., Cağlayan K., 2010. New outbreaks of Plum pox virus in Turkey. International Symposium on Plum pox virus, PPVS 2010 Sofia, Bulgaria.
• Glasa M., Kudela O., Marie-Jeanne V., Labonne G., Dosba F., Quiot J.B., 2001. Characterization of A Natural Recombinant Plum Pox Virus Isolate Detected ın apricot ın Slovakia. XII. International Symposium On Apricot Culture and Decline, Avignon (France) September 10-14, 2001, Organized by INRA.
• Glasa M., Palkovics L., Komínek P., Labonne G., Pittnerová S., Kúdela O., Candresse T., Šubr Z., 2004. Geographically and temporally distant natural recombinant isolates of plum pox virus (PPV) are genetically very similar and form a unique PPV subgroup, J. Genet. Virol., 85, 2671–2681.
• Glasa M., Candresse T., 2008. Plum pox virus, Encyclopedia of Virology, 5 vols (B.W.J. Mahy and M.H.V. Van Regenmortel, Editors), Oxford: Elsevier pp. 238-242.
• Gumus M., Paylan I.C., Matic S., Myrta A., Sipahioglu H.M., Erkan S., 2007. Occurrence and distribution of stone fruit viruses and viroids in commercial plantings of Prunus species in western Anatolia, Turkey. Journal of Plant Pathology 89, 265–268.
• Gürcan K., Ceylan A., Akbulut M., Değirmenci K., 2013a. PPV-T is common in home gardens of Central Anatolia. 2nd International Symposium on Plum Pox Virus, 3-6 September 2013a, Olomouc, Czech Republic, 21.
• Gürcan K., Ceylan A., Akbulut M., Comart S., Akbaş B., Ghaderi M., 2013b. Plum Pox Virus D in Turkey. 2nd International Symposium on Plum Pox Virus, 3-6 September 2013, Olomouc, Czech Republic, 22.
• Gürcan K., Ceylan A., 2016. Strain identification and sequence variability of plum pox virus in Turkey, Turkish Journal of Agriculture and Forestry, 40(5), 746-760.
• Gürcan K., 2017. Bursa’da plum pox virus (Şarka)'ün yaygınlığının ve genetik çeşitliliğinin belirlenmesi. Anadolu Tarım Bilim. Derg./Anadolu J Agr Sci 32, 1-15.
• Gürcan K., Teber S., Çağlayan K., 2019. Further investigation of a genetically divergent group of Plum pox virus-M strain in Turkey, Journal of Plant Pathology, 101(2), 385-391. Gürcan K., Teber S., Candresse T., 2020. Genetic analysis suggests a long and largely isolated evolutionary history of plum pox virus strain D in Turkey. Plant Pathology, 69.2: 370-378.
• Halbrendt J., Nematologist F.R.E.C., 2010. The PPV success story and how to maintain our quarantine-free status. Fruit Times, 29, 1-2.
• James D., Varga A., 2005. Nucleotide sequence analysis of Plum pox virus isolate W3174: evidence of a new strain. Virus Reserach 110: 143-150.
• James D., Varga A., Sanderson D., 2013. Genetic diversity of Plum pox virus: strains, disease and related challenges for control. Can J Plant Pathol 35:431–441.
• Jourdovic M., Janda L., 1963. Morphological, Anathomical and Chemical Changes On The Fruits Of Some Plum Varieties Infected by Virus Plum Pox Disease. Zastita Bilja 14: 301-670.
• Jevremovic D., Paunovic S., 2014. Plum pox virus strains: Diversity and geographical distribution in Serbia. Pestic. Phytomed. (Belgrade), 29(2), 2014, 97–107.
• Kerlan C., Dunez J., 1979. Differenciation biologique et serologique de souches du virus de la Sharka. Annalesde Phytopathologie, 11, 241-250.
• Kimura M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120.
• Koç G., Baloglu S., 2006. Disease Note First Report of Sharka in The Çukurova Region of Turkey. Journal of Plant Pathology, 88(3), S65-S70.
• Kumar S., Stecher G., Tamura K., 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 forbigger datasets. Molecular Biology and Evolution 33:1870-1874.
• Kurçman S., 1973. Nachweis des sharka-virus an aprikosen und pflaumenbaumen aumenbaumen in Ankara. Journal of Turkish Phytopathology, 2: 124-129.
• Myrta A., Boscia D., 2001. Plum pox virus: a risk for the Mediterranean fruit tree industry. Options Méditerranéennes: Série B. Etudes et Recherches, (35), 37-42.
• Myrta A., Varga A., James D., 2006. The complete genome sequence of an El Amar isolate of plum pox virus (PPV) and its phylogenetic relationship to other PPV strains, Archives of Virology, 151, 1189–1198.
• Nemchinov L., Hadidi A. Maiss E., Cambra M., Candresse T., Damsteegt, V., 1996. Sour cherry strainof Plum pox potyvirus (PPV): Molecular and serological evidence for a new subgroup of PPV strains. Phytopathology 86: 1215-1221.
• Nemeth M., Kolber M., 1983. Additional Evidence On Seed Tansmission of Plum pox virus in Apricot, Peach and Plum Proved by ELISA. Acta Horticulturae No. 130. pp.293-300.
• Nemeth M., 1994. History and İmportance of Plum pox In Stone Fruit Production. Bulletin OEPP/EPPO. Bulletin 24, 525-536.
• Oh J.H., Park C.Y., Lee H.K., Yeom Y.A., Lim S.M., Moon J.S., Lee S.H., 2017. First Report of Plum pox virus Strain D Isolate in Peach (Prunus persica) in Korea. Plant Disease, 101(1), 265-265.
• Olmos A., Cambra M., Dasi M.A., Candresse T., Esteban O., Gorris M.T., Asensio M., 1997. Simultaneous detection and typing of plum pox potyvirus (PPV) isolates by heminested-PCR and PCRELISA. J Virol Methods 68: 127-137.
• Palmisano F., Boscia D., Minafra A., Myrta A., Candresse T., 2012. An atypical Albanian isolate of Plum pox virus could be the progenitor of the Marcus strain. In 22nd International Conference on Virus and Other Graft Transmissible Diseases of Fruit Crops, June 3–8, Rome, Book of Abstracts (p. 33).
• Palkovics, L., Burgyán, J., Balázs, E., 1993. Comparative sequence analysis of four complete primary structures of plum pox virus strains, Virus Genes, 7, 339–347.
• Polak J., Pivalova J., Dowler W., Miller W., 2003. Evaluation of American peach cultivars for resistance to Plum pox virus. Plant Protect. Sci. 39: 1-6.
• Revers, F., Garcia, J.A. 2015. Molecular biology of potyviruses. Adv. Virus Res. 92, 101–199. doi: 10.1016/bs.aivir.2014.11.006
• Saitou N., Nei M., 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
• Sahtiyanci S., 1969. Virus de la sharka chez le prunier. Bulletin phytosanitaire FAO, 17, 69.
• Serçe Ç.U., Candresse T., Svanella-Dumas L., Krizbai L., Gazel M., Çağlayan K., 2009. Further characterization of a new recombinant group of Plum pox virus isolates, PPV-T, found in orchards in the Ankara province of Turkey. Virus Research, 142(1-2), 121-126.
• Sertkaya G., Ulubaş Ç., Çağlayan K., 2003. Detection and Characterization of Plum Pox Potyvirus (PPV) by DAS-ELISA and RT-PCR/RFLP Analysis in Turkey. Turkish Journal of Agriculture and Forestry TÜBİTAK. Vol. 27, S.213-220.
• Scholthof, K.B., Adkins, S., Czosnek, H., Palukaitis, P., Jacquot, E., Hohn, T., Hohn, B., Saunders, K., Candresse, T., Ahlquist, P., Hemenway, C., Foster, G.D., 2011. Top 10 plant viruses in molecular plant pathology. Mol Plant P. 12: 938-954.
• Sochor J., Babula P., Adam V., Krska B, Kizek R., 2012. Sharka: The Past, The Present and The Future. Viruses. 4(11): 2853–2901.
• Tamura K., Nei M., Kumar S., 2004. Prospects for inferring very large phylogenies by 4 using the neighbor-joining method. PNAS 101:11030-11035.
• Teber S., Gürcan K., 2016. Recombination analysis of 51 PPV isolates including 10 genomes of PPV-M Istanbul, 3nd International Symposium on Plum Pox Virus, S. 33, 9-13, Antalya, Turkey.
• Teber S., Ceylan A., Gürcan K., Candresse T., Ulubaş Serçe Ç., Akbulut M., Kaymak S., Akbaş B., 2019. Genetic diversity and molecular epidemiology of the T strain of Plum pox virus, Plant Pathology, 68(4), 755-763.
• Thompson, J.D, Higgins, D.G., Gibson, T.J., 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-80.
• Ulubaş-Serçe Ç., Gazel M., Çağlayan K., 2011. Plum pox virus streynlerinin Türkiye‟ deki Dağılımı (Distribution of Plum pox virus strains in Turkey), Türkiye IV. Bitki Koruma Kongresi Bildirileri, Kahramanmaraş, 72.
• Varn M.V., Mavric I., Blazic M., 2004. Influence of PPV infection on the yield and quality of different peach varieties. Lectures and papers presented at the 6th Slovenian Conference on Plant Protection, Zrece, 4-6 March 2003, 258-264.
• Wang A., Sanfacon H., Stobbs L.W., James D., Thompson D., Svircev A.M., Brown D.C.W., 2006. Plum pox virus in Canada: progress in research and future prospects for disease control. Canadian Journal of Plant Pathology 28: 1825196.
• Wetzel T., Candresse T., Ravelonandro M., Dunez J., 1991. A polymerase chain reaction assay adapted to plum pox potyvirus detection. Journal of Virological Methods, 33: 355–365.
• White K.A. 2015. The polymerase slips and PIPO exists. EMBO Rep. 16, 885–886. doi: 10.15252/embr.201540871.
• Yürektürk M., 1984. Marmara Bölgesinde Sert Çekirdekli Meyvelerde Görülen Sharka Hastalığı Üzerinde Araştırmalar. Atatürk Bahçe Kültürleri Araştırma Enstitüsü Yayınları, 37 s.