İzmir ilinde domates ve biber bitkilerini etkileyen tomato spotted wilt virus (TSWV) ve cucumber mosaic virus (CMV) etmenlerinin moleküler karakterizasyonu

Yıl 2023, Cilt: 60 Sayı: 1, 67 - 79, 01.04.2023

Nihan Güneş , İsmail Can Paylan , Mustafa Gümüş

https://doi.org/10.20289/zfdergi.1197925

Cited By: 1

Öz

Amaç: Bu çalışmanın amacı, İzmir'in sebze yetiştirilen önemli ilçelerinde virüs kaynaklı semptomlar gösteren domates ve biber bitkilerinde tomato spotted wilt virus (TSWV) ve cucumber mosaic virus (CMV) enfeksiyonlarının araştırılmasıdır.
Materyal ve Yöntem: Domates ve biber üretim alanlarında 2019 ve 2021 yıllarında sürveyler yapılmış ve toplanan yaprak örneklerinde bu virüslerin enfeksiyon oranları RT-PCR ile belirlenmiştir. TSWV ve CMV izolatlarının GenBank veri tabanından elde edilen diğer izolatlarla benzerlik oranları ve filogenetik ilişkileri belirlenmiştir.
Araştırma Bulguları: Çalışma sonucunda domates bitkilerinin aynı oranda (%21,50) TSWV ve CMV ile enfekteli olduğu belirlenmiştir. Test edilen biber örneklerinin %64,15'inin TSWV ve %25,47'sinin CMV ile enfekteli olduğu tespit edilmiştir. Sonuçlar, TSWV domates izolatlarının nükleokapsid protein gen bölgesinin nükleotid benzerlik oranının %99-96 olduğunu, TSWV biber izolatının ise %100-95 benzerlik gösterdiğini ortaya koymuştur. CMV-domates izolatının kapsid protein gen bölgesi GenBank'taki diğer izolatlarla %98-95 arasında, CMV-biber izolatınınki ise %100-98 arasında nükleotid benzerliğine sahip olmuştur. Ayrıca, CMV izolatları, alt grup IB CMV izolatları ile yakın filogenetik ilişki göstermiştir.
Sonuç: Bu çalışma, İzmir ilinde simptomlu domates ve biber örneklerinde TSWV ve CMV'nin bulaşıklık oranını ve moleküler özelliklerini ortaya koymuştur.

Anahtar Kelimeler

Biber, RT-PCR, patlıcangil, domates, virüs

Destekleyen Kurum

Ege Üniversitesi BAP

Proje Numarası

FGA-2019-20475

Molecular characterization of tomato spotted wilt virus (TSWV) and cucumber mosaic virus (CMV) affecting tomato and pepper crops in Izmir Province

Öz

Objective: The objective of this study was to investigate tomato spotted wilt virus (TSWV) and cucumber mosaic virus (CMV) infections in tomato and pepper plants showing virus-induced symptoms in vegetable growing districts of İzmir, Turkey.
Material and Methods: Surveys were carried out in tomato and pepper plantations in 2019 and 2021, and the incidences of these viruses in the collected leaf samples were determined by RT-PCR. Nucleotide identities and phylogenetic relationships of the TSWV and CMV isolates with other isolates retrieved from the GenBank database were determined.
Results: The results of this study showed that tomato plants were infected at the same rate (21.50%) with TSWV and CMV. Out of the tested pepper samples, 64.15% were infected with TSWV and 25.47% with CMV. The results showed that, the identity rate of nucleoprotein region of TSWV isolates from tomato was 99-96% at nucleotide level while the isolates from pepper showed 100-95% identity. On the other hand, the capsid protein gene region of the tomato isolate of CMV had nucleotide identity rate of 98-95% with other isolates in GenBank, while that of its pepper isolates had 100-98% identity. Also, CMV isolates of this study showed close phylogenetic relationship with the CMV isolates of subgroup IB.
Conclusion: This study revealed the prevalence of TSWV and CMV in symptomatic tomato and pepper samples in İzmir province and some molecular properties of them.

Anahtar Kelimeler

Pepper, solanaceous crops, tomato, virus, RT-PCR

Proje Numarası

FGA-2019-20475

Kaynakça

• Adkins, S., 2000. Tomato spotted wilt virus-positive steps towards negative success. Molecular Plant Pathology, 1 (3): 151-157. https: //doi.org/10.1046/j.1364-3703.2000.00022.x
• Almási, A., K. Nemes & K. Salánki, 2020. Increasing diversity of resistance breaking pepper strains of Tomato spotted wilt virus in the Mediterranean region. Phytopathologia Mediterranea, 59 (2): 385-391. https: //doi.org/10.14601/Phyto-11346
• Arli-Sokmen, M. & M.A. Sevik, 2006. Viruses infecting field-grown tomatoes in Samsun province, Turkey. Archives of Phytopathology and Plant Protection, 39 (4): 283-288. https: //doi.org/10.1080/03235400500222057
• Arli-Sokmen, M., H. Mennan, M.A. Sevik & O. Ecevit, 2005. Occurrence of viruses in field-grown pepper crops and some of their reservoir weed hosts in Samsun, Turkey. Phytoparasitica, 33 (4): 347-358. https: //doi.org/10.1007/BF02981301
• Batuman, O., T.A. Turini, P.V. Oliveira, M.R. Rojas, M. Macedo, H.C. Mellinger, S. Adkins & R.L. Gilbertson, 2017. First report of a resistance-breaking strain of Tomato spotted wilt virus infecting tomatoes with the Sw-5 tospovirus-resistance gene in California. Plant Disease, 101 (4): 637-637. https: //doi.org/10.1094/PDIS-09-16-1371-PDN
• Beşkeçili, M., N. Güneş & M. Gümüş, 2021. Antalya ili Demre ilçesi biber yetiştiriciliğinde Tomato spotted wilt virus (TSWV) ve Cucumber mosaic virus (CMV) etmenlerinin yaygınlığının belirlenmesi, Ege Universitesi Ziraat Fakültesi Dergisi, 58 (3): 399-405. http: //doi.org/10.20289/zfdergi.799432
• Canto, T., D.A. Prior, K.H Hellwald, K.J. Oparka & P. Palukaitis, 1997. Characterization of Cucumber mosaic virus. Virology, 237 (2): 237-248. https: //doi.org/10.1006/viro.1997.8804
• Chapman, E.J., P. Hilson & T.L. German, 2003. Association of L protein and in vitro Tomato spotted wilt virus RNA-Dependent RNA polymerase activity. Intervirology, 46 (3): 177-181. https: //doi.org/10.1159/000071459
• Debreczeni, D.E., C. López, J. Aramburu, J.A. Darós, S. Soler, L. Galipienso, R.B. Falk & L. Rubio, 2015. Complete sequence of three different biotypes of Tomato spotted wilt virus (wild type, tomato Sw-5 resistance breaking and pepper Tsw resistance-breaking) from Spain. Archives of Virology, 160 (8): 2117-2123. https: //doi.org/10.1007/s00705-015-2453-8
• Deligoz, I., Arli Sokmen M. & S. Sari, 2014. First report of resistance breaking strain of Tomato spotted wilt virus (Tospovirus; Bunyaviridae) on resistant sweetpepper cultivars in Turkey. New Disease Reports 30: 26. DOI: 10.5197/j.2044-0588.2014.030.026
• Faggioli, F., L. Ferretti, G. Albanese, R. Sciarroni, G. Pasquini, V. Lumia & M. Barba, 2005. Distribution of olive tree viruses in Italy as revealed by one-step RT-PCR. Journal of Plant Pathology, 49-55.
• FAO, 2020. World tomato and pepper production list. (Web site: https: //www.fao.org/faostat/en/#home) (Access date: January 2022.)
• Fidan, H. & N. Sari, 2019. Molecular characterization of resistance-breaking Tomato spotted wilt virus (TSWV) isolate medium segment in tomato. Applied Ecology and Environmental Research, 17 (2): 5321-5339. https: //doi.org/10.15666/aeer/1702_53215339
• Foissac, X., L. Svanella-Dumas, M.J. Dulucq, T. Candresse & P. Gentit, 2001. Polyvalent detection in fruit tree tricho, capillo and foveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR). Acta Horticulturae, 550: 37-43. https: //doi.org/10.17660/ActaHortic.2001.550.2
• Gal-On, A., T. Canto & P. Palukaitis, 2000. Characterisation of genetically modified Cucumber mosaic virus expressing histidine-tagged 1a and 2a proteins. Archives of Virology, 145 (1): 37-50. https: //doi.org/10.1007/s007050050003
• Goto, K., T. Kobori, Y. Kosaka, T. Natsuaki & C. Masuta, 2007. Characterization of silencing suppressor 2b Cucumber mosaic virus based on examination of its small RNA-binding abilities. Plant Cell Physiology, 48: 1050-1060. https: //doi.org/10.1093/pcp/pcm074
• Gümüş, M., 1998. The Studies on The Detection of The Viruses and Their Incidence in Peppers in İzmir Province and the Determination of the Reactions of Certain Pepper Cultivars to these Viruses. Ege University, Graduate School of Natural and Applied Science, (Unpublished) PhD Thesis, İzmir, Turkey, 118 pp (in Turkish with Abstract in English).
• Güneş, N. & M. Gümüş, 2019. Detection and Characterization of Tomato spotted wilt virus and Cucumber mosaic virus on pepper growing areas in Antalya. Journal of Agricultural Sciences, 25 (3): 259-271. https: //doi.org/10.15832/ankutbd.499144
• Hristova, D., O. Karadjova, M. Yankulova, C. Heinze & G. Adam, 2001. A survey of tospoviruses in Bulgaria. Journal of Phytopathology, 149 (11-12): 745-749. https: //doi.org/10.1046/j.1439-0434.2001.00694.x
• Jiang, L., Y. Huang, L. Sun, B. Wang, M. Zhu, J. Li, C. Huang, Y. Liu, F. Li, Y. Liu, J. Dong, Z. Zhang & X. Tao, 2017. Occurrence and diversity of Tomato spotted wilt virus isolates breaking the Tsw resistance gene of Capsicum chinense in Yunnan, southwest China. Plant Pathology, 66 (6): 980-989. https: //doi.org/10.1111/ppa.12645
• Karavina, C., S. Ximba, J.D. Ibaba & A. Gubba, 2016. First report of a mixed infection of Potato virus Y and Tomato spotted wilt virus on pepper (Capsicum annuum) in Zimbabwe. Plant Disease, 100 (7): 1513-151. https: //doi.org/10.1094/PDIS-02-16-0185-PDN
• Kumar, S., G. Stecher, M. Li, C. Knyaz & K. Tamura, 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35: 1547-1549. https: //doi.org/10.1093/molbev/msy096
• Lee, J.S., W.K. Cho, M.K. Kim, H.R. Kwak, H.S. Choi & K.H. Kim, 2011. Complete genome sequences of three Tomato spotted wilt virus isolates from tomato and pepper plants in Korea and their phylogenetic relationship to other TSWV isolates. Archives of Virology, 156 (4): 725-728. https: //doi.org/10.1007/s00705-011-0935-x
• Li, J., Z. Feng, J. Wu, Y. Huang, G. Lu, M. Zhu, B. Wang, X. Mao & X. Tao, 2015. Structure and function analysis of nucleocapsid protein of Tomato spotted wilt virus interacting with RNA using homology modeling. Journal of Biological Chemistry, 290 (7): 3950-3961. https: //doi.org/10.1074/jbc.M114.604678
• Li, W., D.J. Lewandowski, M.E. Hilf & S. Adkins, 2009. Identification of domains of the Tomato spotted wilt virus NSm protein involved in tubule formation, movement and symptomatology. Virology, 390: 110-121. https: //doi.org/10.1016/j.virol.2009.04.027
• Lin, H.X., L. Rubio, A. Smythe, M. Jiminez & B.W. Falk, 2003. Genetic diversity and biological variation among California isolates of Cucumber mosaic virus. Journal of General Virology, 84 (1): 249-258. https: //doi.org/10.1099/vir.0.18673-0
• Loebenstein, G. & H.‬ Lecoq, 2012. “Major Tomato Viruses in the Mediterranean Basin, 31-67”. In: Advances in Virus Research Viruses and Virus Diseases of the Vegetables in the Mediterranean Basin (Eds. G. Loebenstein & H. Lecoq‬). Academic Press-Elsevier. Amsterdam, The Netharlands, 595 pp.
• Macharia, I., D. Backhouse, E.M. Ateka, S.B. Wu, J. Harvey, M. Njahira & R.A. Skilton, 2015. Distribution and genetic diversity of Tomato spotted wilt virus following an incursion into Kenya. Annals of Applied Biology, 166 (3): 520-529. https: //doi.org/10.1111/aab.12201
• Morca, A.F., A. Çelik, S. Coşkan, A.I. Santosa & B. Akbaş, 2022. Population analysis on Tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey. Physiological and Molecular Plant Pathology, 101786. https: //doi.org/10.1016/j.pmpp.2022.101786
• Nagata, T., A.K. Inoue-Nagata, J. van Lent, R. Goldbach & D. Peters, 2002. Factors determining vector competence and speci- ficity for transmission of Tomato spotted wilt virus. Journal of General Virology, 83: 663-667. https: //doi.org/10.1099/0022-1317-83-3-663
• Nour, S.M., M. Maleki & T. Ghotbi, 2013. Biological and serological detection of TSWV on three commercial cultivars Chrysanthemum morifolium in Markazi province of Iran. Annals of Biological Research, 4 (4): 112-119.
• Parrella, G., P. Gognalons, K. Gebre-Selassie, C. Vovlas & G. Marchoux, 2003. An update of the host range of Tomato spotted wilt virus. Journal of Plant Pathology, 227-264.
• Phatsaman, T., S. Wasee & R. Hongprayoon, 2021. Incidence and distribution of pepper-infecting viruses in Thailand. Journal of the International Society for Southeast Asian Agricultural Sciences, 27 (2): 1-13.
• Pinto, Z.V., J.A.M. Rezende, V.A. Yuki & S.M.D.S. Piedade, 2008. Ability of Aphis gossypii and Myzus persicae to transmit Cucumber mosaic virus in single and mixed infection with two potyviruses to zucchini squash. Summa Phytopathologica, 34 (2): 183-185.
• Rivera-Toro, D.M., J.C. Vaca-Vaca & K. López-López, 2020. Detection and molecular characterization of the Cucumber mosaic virus in chili pepper (Capsicum spp. L.) crops. Agronomía Colombiana, 38 (2): 218-225. https: //doi.org/10.15446/agron.colomb.v38n2.82975
• Roggero, P., V. Masenga & L. Tavella, 2002. Field isolates of Tomato spotted wilt virus overcoming resistance in pepper and their spread to other hosts in Italy. Plant Disease, 86 (9): 950-954. https: //doi.org/10.1094/PDIS.2002.86.9.950
• Roossinck, M.J., 2002. Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses. Journal of Virology, 76 (7): 3382-3387. https: //doi.org/10.1128/JVI.76.7.3382-3387.2002
• Scholthof, K.B.G., S. Adkins, H. Czosnek, P. Palukaitis, E. Jacquot, T. Hohn, B. Hohn, K. Saunders, T. Candresse, P. Ahlquist, C. Hemenway & G.D. Foster, 2011. Top 10 plant viruses in molecular plant pathology. Molecular Plant Pathology, 12 (9): 938-954. https: //doi.org/10.1111/J.1364-3703.2011.00752.X
• Sin, S.H., B.C. McNulty, G.G. Kennedy & J.W. Moyer, 2005. Viral genetic determinants for thrips transmission of Tomato spotted wilt virus. Proceedings of the National Academy of Sciences, 102 (14): 5168-5173. https: //doi.org/10.1073/pnas.0407354102
• Takeda, A., K. Sugiyam, H. Nagano, M. Mori, M. Kaido, K. Mise, S. Tsuda & T. Okuno, 2002. Identification of a novel RNA silencing suppressor, NSs protein of Tomato spotted wilt virus. FEBS Letters, 532: 75-79. https: //doi.org/10.1016/S0014-5793 (02)03632-3
• Tamura, K. & M. Nei, 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526. https: //doi.org/10.1093/oxfordjournals.molbev.a040023
• Thompson, J.R., E. Buratti, M. de Wispelaere & M. Tepfer, 2008. Structural and functional characterization of the 5′ region of subgenomic RNA5 of Cucumber mosaic virus. Journal of General Virology, 89 (7): 1729-1738. https: //doi.org/10.1099/vir.0.2008/001057-0
• TUİK, 2022. Turkey tomato and pepper production list. (Web site: https: //biruni.tuik.gov.tr/medas/?kn=92&locale=tr.) (Access date: January 2022.)
• Uzunoğulları, N. & M. Gümüş, 2015. Detection of Cucumber mosaic virus (Cucumber mosaic virus, CMV) causing natural infection on some cultured plants in Marmara Region. Trakya University Journal of Natural Sciences, 16 (1): 9-15 (in Turkish with an abstract in English).
• Vinodhini, J., L. Rajendran, R. Abirami & G. Karthikeyan, 2021. Co-existence of chlorosis inducing strain of Cucumber mosaic virus with tospoviruses on hot pepper (Capsicum annuum) in India. Scientific Reports, 11 (1): 1-9. https: //doi.org/10.1038/s41598-021-88282-9
• Waweru, B.W., D.C. Kilalo, J.W. Kimenju, P. Rukundo & D.W. Miano, 2020. Evaluation of hot pepper (Capsicum spp.) genotypes for resi‐stance to viruses and aphids in Rwanda. Advances in Horticultural Science, 34 (4): 397-412. https: //doi.org/10.13128/ahsc8094
• Yardımcı, N. & H. Eryiğit, 2006. Identification of Cucumber mosaic virus in tomato (Lycopersicon esculentum) growing areas in the north‐west Mediterranean region of Turkey. New Zealand Journal of Crop and Horticultural Science, 34 (2): 173-175. https: //doi.org/10.1080/01140671.2006.9514403