Düzce İlinde Kabak Bitkilerini Enfekte Eden Virüslerin Tespiti ve Moleküler Karakterizasyonu

Abstract

Bu çalışma, vektör aktivitesine ve virüs bulaşmasına son derece elverişli çevresel koşullara sahip Türkiye'nin Karadeniz Bölgesi'nde yer alan Düzce ilinde kabak bitkilerini enfekte eden başlıca virüslerin yaygınlığı, dağılımı ve moleküler çeşitliliğine ilişkin ilk kapsamlı değerlendirmeyi sunmaktadır. Arazi çalışmalarında toplam 33 simptomatik örnek toplanmış ve ekonomik açıdan önemli Cucumovirus CMV (Cucumber mosaic virus; CMV), Potyvirus citrulli (Watermelon mosaic virus; WMV), Potyvirus cucurbitaflavitesselati (Zucchini yellow mosaic virus; ZYMV), Alphaendornavirus meloense (Cucumis melo endornavirus; CmEV) ve Tobamovirus viridimaculae (Cucumber green mottle mosaic virus; CGMMV) olmak üzere beş virüs için moleküler testlerle taranmıştır. Örneklerin %87,9'unda virüs enfeksiyonu tespit edilmiş olup, karışık enfeksiyonların yüksek oranda görüldüğü belirlenmiştir. Örneklerde en yaygın virüs olarak CMV (25 bitkide) bulunurken, en az bulunan virüs ise CmEV (3 bitkide) olmuştur, WMV ise 14 bitkide tespit edilmiştir. ZYMV ve CGMMV ise tespit edilmemiştir. Filogenetik ve benzerlik analizleri, Düzce izolatlarının küresel olarak dağılmış izolatlar ile yakından ilişkili olduğunu ortaya koymuştur. CMV izolatı Ia alt grubunda, WMV izolatı ise EM1 grubundaki izolatlar ile kümelenmiştir, bu da yerel ve uluslararası virüs popülasyonları arasında potansiyel bir bağlantı olduğunu düşündürmüştür. Karışık enfeksiyonların sıklığı ve CMV'nin baskınlığı, muhtemelen elverişli ekolojik habitat koşullar ve etkili vektör aracılı bulaşma tarafından yönlendirilen kompleks ve dinamik bir viral popülasyon yapısını göstermektedir.

Keywords

• RT-PCR
• Benzerlik
• Filogenetik

Detection and Molecular Characterization of Viruses Infecting Squash Plants in Düzce Province, Türkiye

Abstract

This study provides the first comprehensive assessment of the occurrence, distribution, and molecular diversity of major viruses infecting squash plants in Düzce province, located in the humid Black Sea Region of Türkiye, where environmental conditions are highly conducive to vector activity and virus transmission. A total of 33 symptomatic samples were collected during field surveys and screened by molecular assays for five economically important viruses: Cucumovirus CMV (Cucumber mosaic virus; CMV), Potyvirus citrulli (Watermelon mosaic virus; WMV), Potyvirus cucurbitaflavitesselati (Zucchini yellow mosaic virus; ZYMV), Alphaendornavirus meloense (Cucumis melo endornavirus; CmEV), and Tobamovirus viridimaculae (Cucumber green mottle mosaic virus; CGMMV). Virus infection was detected in 87.9% of the samples, with a high prevalence of mixed infections. CMV was the dominant virus (25/33), followed by WMV (14/33) and CmEV (3/33), whereas ZYMV and CGMMV were not detected. Phylogenetic and sequence identity analyses revealed that the Düzce isolates were closely related to globally distributed strains, with the CMV isolate clustering within subgroup Ia and the WMV isolate within the EM1 lineage, suggesting potential connectivity between local and international virus populations. The frequency of co-infections and the dominance of CMV indicate a complex and dynamic viral population structure, likely driven by favorable ecological conditions and efficient vector-mediated transmission.

Keywords

• RT-PCR
• Similarity
• Phylogenetics

References

1. Akdura, N., & Culal-Kilic, H. (2022). Molecular characterizations of cucumber mosaic virus and tomato mosaic virus isolates in Hakkari Turkey. Fresenius Environmental Bulletin, 31(8B), 8993–9004.
2. Ali, A., Mohammad, O., & Khattab, A. (2012). Distribution of viruses infecting cucurbit crops and isolation of potential new virus-like sequences from weeds in Oklahoma. Plant Disease, 96(2), 243-248.
3. Aydın, Ö., Morca, A. F., Coşkan, S., Santosa, A. I., & Çelik, A. (2025). A study of the P1 gene in Türkiye for genetic diversity of watermelon mosaic virus. Journal of Crop Health, 77(3), 97.
4. Balsak, S. C. (2025). Investigation of virus and viroid diseases in cucurbits. Yuzuncu Yıl University Journal of Agricultural Sciences, 35(2), 369–380.
5. Biltekin, A., & Akdura, N. (2024). Detection of Cucumber Mosaic Virus (CMV) in Cucurbits by TaqMan Real-Time RT-PCR in Hakkari Province, Türkiye. Turkish Journal of Agricultural and Natural Sciences, 11(3), 825-834.
6. Can, S., Baloğlu, S., & Kamberoğlu, M. A. (2025). Örtü altında yetiştirilen biberlerde hıyar mozaik virüsü (Cucumber mosaic virus, CMV)’nün saptanması ve karakterizasyonu. Çukurova Tarım ve Gıda Bilimleri Dergisi, 40(2), 510–525.
7. Çandar, A., Aydın, A., Şavkan, A. N., Güngör, R., & Başak, H. (2026). Detection and Incidence of Cucurbit Viruses in Kırşehir Province, Türkiye. Plant Protection Bulletin, 66(1), 26-38.
8. Çulal-Kılıç, H., & Kahraman, A. (2024). Burdur ili Kabakgillerinde Watermelon mosaic virus ve Cucumber mosaic virus' unun Belirlenmesi. Duzce University Journal of Science & Technology, 12(2).

9. de Moya‐Ruiz, C., Juárez, M., & Gómez, P. (2025). Revealing hidden viruses inducing similar yellowing symptoms or remaining asymptomatic in cucurbit crops. Plant Pathology, 74(1), 270-282.
10. Desbiez, C., Wipf-Scheibel, C., Millot, P., Berthier, K., Girardot, G., Gognalons, P., et al., (2020). Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area. Virus Research, 286, 198042.
11. Güller, A., Demirel, S., Usta, M., & Korkmaz, G. (2024a). Genetic diversity of cucumber mosaic virus in cucumber plants grown in Diyarbakır province. Türk Doğa ve Fen Dergisi, 13(1), 1–6.
12. Güller, A., Usta, M., Korkmaz, G., & Demirel, S. (2024b). In silico and molecular analysis of some mosaic diseases on cucurbit plants in Iğdır province, Türkiye. Turkish Journal of Agricultural and Natural Sciences, 11(1), 90–103. Jones, R. A. C. (2016). Future scenarios for plant virus pathogens as climate change progresses. Advances in Virus Research, 95, 87–147.
13. Kamberoğlu, M. A., & Keçe, M. A. (2016). Doğu Akdeniz Bölgesi’nde karpuz yetiştirilen alanlarda karpuz mozayik virüsü (WMV-2)’nün biyolojik, serolojik ve moleküler olarak belirlenmesi. Tekirdağ Ziraat Fakültesi Dergisi, 13(3), 156-164.
14. Kamberoglu, M. A., Caliskan, A. F., & Desbiez, C. (2016). Current status of some cucurbit viruses in Cukurova region (Adana and Mersin provinces) of Turkey and molecular characterization of zucchini yellow mosaic virus isolates. Romanian Biotechnological Letters, 21(4), 11709–11719.
15. Karabulut, D., & Koklu, G. (2025). Determination and molecular characterization of watermelon mosaic virus in cucurbit plants in Tekirdag province in Türkiye. Applied Ecology & Environmental Research, 23(1).
16. Karanfil, A. (2021). Prevalence and molecular characterization of Cucumber mosaic virus isolates infecting tomato plants in Marmara region of Turkey. Plant Protection Bulletin, 61(4), 19-25.
17. Karanfil, A., & Korkmaz, S. (2020). First report of Cucumis melo endornavirus with a new host, the gherkin (Cucumis anguria Linn.), in Turkey. Trakya University Journal of Natural Sciences, 21(1), 63–67.
18. Karanfil, A., & Korkmaz, S. (2021). Güney Marmara Bölgesi kabakgil üretim alanlarında cucumber mosaic virus enfeksiyonunun tespiti ve kılıf protein gen diziliminin filogenetik analizi. Journal of Agriculture Faculty of Ege University, 58(2), 239-246.
19. Karanfil, A., Randa-Zelyüt, F., & Korkmaz, S. (2023a). Population structure and genetic diversity of tobacco mild green mosaic virus variants in Western Anatolia of Turkey. Physiological and Molecular Plant Pathology, 125, 102008.
20. Karanfil, A., Zelyüt, F. R., & Korkmaz, S. (2023b). Güney Marmara bölgesi kabakgil üretim alanlarında Cucumis melo endornavirus enfeksiyonunun belirlenmesi ve izolatların moleküler karakterizasyonu. Turkish Journal of Agricultural and Natural Sciences, 10(4), 1001–1008.
21. Khanal, V., Wells, H., & Ali, A. (2021). High prevalence of three potyviruses infecting cucurbits in Oklahoma and phylogenetic analysis of cucurbit aphid-borne yellows virus isolated from pumpkins. Pathogens, 10(1), 53.
22. Lecoq, H. (2003). Cucurbits. In Virus and virus-like diseases of major crops in developing countries (pp. 665-688). Dordrecht: Springer Netherlands.
23. Lecoq, H., & Desbiez, C. (2012). Viruses of cucurbit crops in the Mediterranean region: an ever-changing picture. In Advances in virus research (Vol. 84, pp. 67-126). Academic Press.
24. Letschert, B., Adam, G., Lesemann, D. E., Willingmann, P., & Heinze, C. (2002). Detection and differentiation of serologically cross-reacting tobamoviruses of economical importance by RT-PCR and RT-PCR-RFLP. Journal of virological methods, 106(1), 1-10.
25. Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J., & Kinard, G. (2008). A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of virological methods, 154(1-2), 48-55.
26. Morca, A. F., Coşkan, S., Öncü, F., Akbaş, B., Santosa, A. I., Yeşil, S., & Çelik, A. (2025). Genetic diversity and phylogenetic analysis of watermelon mosaic virus in Türkiye: Insights into emerging and classic populations. Current Microbiology, 82(7), 298.
27. Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS one, 9(9), e108277.
28. Mulholland, S. (2022). Cucurbit production systems in Australia and biosecurity risks associated with viral pathogens. Australasian Plant Pathology, 51(6), 587-596.
29. Ohshima, K., Matsumoto, K., Yasaka, R., Nishiyama, M., Soejima, K., Korkmaz, S., et al., (2016). Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology, 487, 188-197.
30. Özer, M., Sipahioğlu, H. M., Usta, M., & Fidan, H. (2012). Cloning and sequencing of coat protein gene of zucchini yellow mosaic virus isolated from squash and muskmelon in Turkey. Turkish Journal of Biology, 36(4), 423–429.
31. Provvidenti, R. (1996). Diseases caused by viruses. In: Zitter, Hopkins, Thomas (eds), Compendium of Cucurbit Diseases, American Phytopathological Society, St. Paul, MN, USA pp. 25-45.
32. Quito-Avila, D. F., Peralta, E. L., Martin, R. R., Ibarra, M. A., Alvarez, R. A., Mendoza, A., et al., (2014). Detection and occurrence of melon yellow spot virus in Ecuador: an emerging threat to cucurbit production in the region. European journal of plant pathology, 140(2), 193-197.
33. Randa-Zelyüt, F., & Karanfil, A. (2025). Multilocus sequence typing of “Candidatus Phytoplasma solani” and detection of RNA viruses infecting cucurbits in the Marmara region, Türkiye. Plant Pathology, 74(6), 1905–1914.
34. Randa-Zelyüt, F., Fox, A., & Karanfil, A. (2023). Population genetic dynamics of southern tomato virus from Turkey. Journal of Plant Pathology, 105(1), 211–224.
35. Sastry, S. K., & Zitter, T. A. (2014). Management of virus and viroid diseases of crops in the tropics. In S. K. Sastry & T. A. Zitter (Eds.), Plant virus and viroid diseases in the tropics (Vol. 2, pp. 149–480). Springer.
36. Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38(7), 3022-3027.
37. Topkaya, S. (2020). Kastamonu ili ve çevresinde kabakgil yetiştirilen alanlarda enfeksiyon oluşturan viral etmenlerin saptanması. Gaziosmanpaşa Bilimsel Araştırma Dergisi, 9(1), 65–72.
38. Topkaya, S., Desbiez, C., & Ertunc, F. (2019). Presence of cucurbit viruses in Ankara and Antalya province and molecular characterization of coat protein gene of zucchini yellow mosaic virus Turkish isolates. Fresenius Environmental Bulletin, 28(4), 2442–2449.