In Silico and Molecular Analysis of Some Mosaic Diseases on Cucurbit Plants in Iğdır Province, TÜrkiye

Year 2024, Volume: 11 Issue: 1, 90 - 103, 28.01.2024

Abdullah Güller Mustafa Usta Gülüstan Korkmaz Serap Demirel

https://doi.org/10.30910/turkjans.1387512

Abstract

Cucumber mosaic cucumovirus (CMV) and Watermelon mosaic potyvirus (WMV) are plant viruses with positive single-stranded RNA genome that infect cucurbits and cause economic losses. Both viruses cause especially mosaic pattern and deformities in leaves, in cucurbit plants. The leaves of 23 melon and 28 watermelon plants showing such symptoms were sampled from different regions of Iğdır province. Samples with and without symptoms were tested by the Reverse Transcription Polymerase Chain Reaction (RT-PCR) using coat protein gene (CP)-specific primers. Polymerization tests amplified DNA fragments of the expected size for CMV and WMV. Some fragments with positive results were purified, bacterial cloned, nucleotide sequences revealed and registered in the GeneBank (NCBI). Sequence analyzes showed that it contained 593 bp and 822 bp for CMV and WMV, corresponding to the partial CP gene. Phylogenetic relationships with isolates from different geographical regions and plant material were investigated for both viruses. The generated phylogenetic tree confirmed that CMV-Iğdır isolate was in Group I and subgroup B, and WMV-Iğdır isolates were in different groups. In addition, coat proteins of virus isolates were characterized by in silico tools.
In the current study, the presence WMV of and CMV in watermelon and melon was determined for the first time in Iğdır province, and group/subgroup assignments of CMV were revealed.

Keywords

Cucumber mosaic cucumovirus, In silico analysis, Molecular characterization, RT-PCR, Watermelon mosaic potyvirus

Project Number

Çalışmanın projesi bulunmamaktadır

Iğdir İli Kabakgil Bitkilerinde Bazı Mozaik Hastalıklarının In Siliko ve Moleküler Analizi

Abstract

Cucumber mosaic cucumovirus (CMV) ve Watermelon mosaic potyvirus (WMV) kabakgilleri infekteleyen ve ekonomik kayıplara neden pozitif tek iplikli RNA genomuna sahip bitki virüslerdir. Her iki virüs kabakgil bitkilerde başta mozaik deseni ve yapraklarda şekil bozukluklarına yol açar. Bu tür belirtiler gösteren 23 kavun ve 28 karpuz bitkisinin yaprakları Iğdır ilinin farklı bölgelerinden örneklendirilmiştir. Simptomlu ve simptomsuz örnekler Reverse Transkripsiyon Polimeraz Zircir Reaksiyonu (RT-PCR) tarafından kılıf protein geni (CP) spesifik primerler kullanılarak testlenmiştir. Polimerizasyon testleri, CMV ve WMV için beklenen boyutta DNA fragmentleri amplifiye etmiştir. Pozitif sonuçlu bazı fragmentler saflaştırılmış, bakteriyel klonlaması gerçekleştirilmiş, nükleotit dizileri ortaya çıkarılmış ve gen bankasına (NCBI) kaydedilmiştir. Dizi analizleri, CMV ve WMV’nin kısmi kılıf protein dizilerine karşılık gelen 593 bp ve 822 bp nükleotit içerdiğini göstermiştir. Her iki virüs için farklı coğrafi bölgelerden sağlanan izolatlar nükleotit sekanslarına dayalı olarak filogenetik ilişkileri ortaya konmuştur. Oluşturulan filogenetik ağaç CMV-Iğdır izolatının Grup I ve alt grup B’de olduğunu ve WMV-Iğdır izolatlarının ise farklı gruplarda yer aldığını doğrulamıştır. Ayrıca virus izolatlarının kılıf proteinleri in silico araçlar ile karakterize edilmiştir.
Bu çalışmayla Iğdır ilinde moleküler olarak ilk kez kavunda ve karpuzda CMV ile WMV varlığı saptanmış ve CMV’nin grup/altgrup atamaları gerçekleştirilmiştir.

Keywords

Hıyar mozaik virüsü, In silico analiz, Karpuz mozaik virüsü, Moleküler karaterizasyon, RT-PCR

Ethical Statement

-

Supporting Institution

-

Project Number

Çalışmanın projesi bulunmamaktadır

Thanks

Dergi yönteici ve sekreteryasına teşekkür ediyorum

References

• Aguiar, R., Alves, G.B., Queıroz, A.P., Nascimento, I., Lima, M. 2018. Evaluation of Weeds as Virus Reservoirs in Watermelon Crops. Planta Daninha, 36. 10.1590/s0100-83582018360100032.
• 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.
• Blancard D., Lecoq H., Pitrat M., 1994. A Colour Atlas of Cucurbit Diseases: Observation, Identification and Control. Manson Publishing Ltd, 299 pp.
• Chare, E. R., Holmes, E. C. 2006. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch. Virol., 151, 933–946.
• Cohen S., Nitzany F.E., 1963. Identity of viruses affecting cucurbits in Israel. Phytopathology, Worcester, Mass. 53.
• Crescenzi, A., Fanigliulo, A., Comes, S., Masenga, V., Pacella, R., Piazzolla, P. 2001. Necrosis of watermelon caused by Watermelon mosaic virus. J. Plant Pathol., 83(3), 227. doi: 10.2307/41998070.
• DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, Palo Alto
• Desbiez, C., Joannon, B., Wipf-Scheibel, C., Chandeysson, C., Lecoq, H. 2011. Recombination in natural populations of watermelon mosaic virus: new agronomic threat or damp squib? J. Gen. Virol., 92(8), 1939-1948. doi: 10.1099/vir.0.031401-0.
• Desbiez, C., Joannon, B., Wipf-Scheibel, C., Chandeysson, C., Lecoq, H. 2009. Emergence of new strains of Watermelon mosaic virus in South-eastern France: Evidence for limited spread but rapid local population shift. Virus Res., 141, 201-208.
• Desbiez, C., Lecoq, H. 2008. Evidence for multiple intraspecific recombinants in natural populations of Watermelon mosaic virus (WMV, Potyvirus). Arch. Virol., 153, 1749-1754.
• Desbiez, C., Costa, C., Wipf-Scheibel, C., Girard, M., Lecoq, H. 2007. Serological and molecular variability of Watermelon mosaic virus (genus Potyvirus). Arch. Virol., 152, 775-781.
• Fabre, F., Chaduf, J., Costa, C., Lecoq, H., Desbiez, C. 2010. Asymmetrical overinfection as a process of plant virus emergence. J. Theor. Biol., 265, 377-388. FAOSTAT Data. 2007. Available at: http://www.faostat.fao.org. (Accessed on Dec 2007).
• Foissac, L., Gentit, P., Svanetia-Dumas, L., Dulucq, M. J., Candresse, T. 2001. Polyvalent detection of fruit tree tricho, capillo, and foveaviruses by nested RT-PCR using degenerated and inosine-containing primers (PDO RT-PCR). Acta Hortic., 550, 37-43.
• Garcia-Andres, S., Accotto, G. P., Navas-Castillo, J., Moriones, E. 2007. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin. Virology, 359, 302-312.
• Glasa, M., Bananej, K., Predajňa, L., Vahdat, A. 2011. Genetic diversity of watermelon mosaic virus in Slovakia and Iran shows distinct pattern. Plant Dis., 95(1), 38-42.
• Hamza, E. S., Al-Naggar, A. M., El-Shabrawi, H. M., Tolba, I. H. 2022. Characteristics of Cucumber Mosaic Virus Isolates Infecting Cucurbits in Egypt. Al-Azhar J. Agric. Res., 47(1), 172-184.
• Jeffrey, C., 1990. Systematics of the Cucurbitaceae: an overview. In: (eds. Bates DM, Robinson RW, Jeffrey C) pp 3-9, Biology and Utilization of the Cucurbitaceae. Cornell University Press, Ithaca, NY, USA.
• Juárez M., Rabádan M.P., Martínez L.D., Tayahi M., Grande-Pérez A., Gómez P. 2019. Natural hosts and genetic diversity of the emerging Tomato leaf curl New Delhi virus in Spain. Front. Microbiol. 10: 140. doi: 10.3389/fmicb.2019.00140.
• Karanfil A., Soylu B., Korkmaz S. 2016. Çanakkale ili ve ilçelerindeki soğanlı süs bitkilerinde Hıyar mozaik virüsü enfeksiyonunun serolojik ve moleküler yöntemler ile araştırılması. Trakya Univ. J. Nat. Sci. 17(2): 105-110.
• Karanfil A., Korkmaz S. 2017. Detection and molecular characterization based on coat protein gene of Cucumber mosaic virus (CMV) from cowpea production fields of Çanakkale province in Turkey. Bitki Koruma Bülteni. 57(3): 293–304.
• Karanfil, A., Korkmaz, S. 2021. Güney Marmara Bölgesi kabakgil üretim alanlarında cucumber mosaic virus enfeksiyonunun tespiti ve kılıf protein gen diziliminin filogenetik analizi. Ege Üniversitesi Ziraat Fakültesi Dergisi, 58(2), 239-246.
• Karanfil, A. 2022. Marmara Bölgesi Kabak Üretim Alanlarında Tobacco Mosaic Virus İzolatlarının Yaygınlığı ve Moleküler Karakterizasyonu. Journal of Advanced Research in Natural and Applied Sciences, 8(2), 163-170. " Kelley LA, Sternberg MJ. 2009. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4:363–371.
• Kızmaz M.Z., Sağır A., Baloğlu S. 2016. Diyarbakır ve Mardin İlleri Kabakgil Üretim Alanlarında Görülen Viral Hastalıkların Yaygınlıklarının ve Etmenlerinin Belirlenmesi. Ege Univ. Ziraat Fak. Derg. 53(4): 397-406.
• Köklü G., Yilmaz, Ö., 2006. Occurrence of cucurbit viruses on field-grown melon and watermelon in the Thrace region of Turkey. Phytoprotection, 87, 123–130. DOI: 10.7202/015854ar.
• Lecoq, H., Desbiez, C., 2008. Watermelon mosaic virus and Zucchini yellow mosaic virus. Encyclopedia of Virology, 433–440. DOI: 10.1016/B978-012374410-4.00740-8.
• Lecoq, H., Desbiez, C., 2012. Viruses of Cucurbit Crops in the Mediterranean Region. An Ever-Changing Picture. Adv. Virus Res. 84: 67–126.
• Lecoq, H., 1992a. Les virus des cultures de melon et de courgette de plein champ (I). PHM Rev. Hortic. 323:23–27.
• Lecoq, H., 1992b. Les virus des cultures de melon et de courgette de plein champ (II). PHM Rev. Hortic. 324:15–25.Loebenstein G. (Gad), Lecoq H., 2012. Viruses and Virus Diseases of the Vegetables in the Mediterranean Basin. Academic Press: San Diego, California, United States of America, 570 pp.
• Luis-Arteaga, M., Alvarez, J. M., Alonso-Prados, J. L., Bernal, J. J., Garcia-Arenal, F., Lavina, A., Batlle, A., Moriones, E. 1998. Occurrence, distribution, and relative incidence of mosaic viruses infecting field-grown melon in Spain. Plant Dis., 82, 979-982.
• Massumi, H., Samei, A., Pour, A.H., Shaabanian, M., Rahimian, H. 2007. Occurrence, Distrubution, and Relative Incidence of Seven Viruses Infecting Greenhouse-Grown Cucurbits in Iran. Plant Dis., 91:159-163.
• Mohammadi K., Hajizadeh M., Koolivand D. 2016. Detection and identification of four vegetable fruit viruses in West and Northwest of Iran. Iran J. Plant Pathol., 52 (2), 279-288.
• Moreno, I.M., Malpica, J.M., Dıaz-Pendón, J.A., Moriones, E., Fraile, A., Garcia-Arenal, F. 2004. Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain. Virology, 318(1), 451-460.
• Nagy, P.D. 2008. Recombination in Plant RNA Viruses. In: Roossinck, MJ, editor. Plant Virus Evolution. Springer Berlin Heidelberg. p 133-156.
• Nouri, S, Arevalo, R, Falk, B.W., Groves, R.L. 2014. Genetic structure and molecular variability of Cucumber mosaic virus isolates in the United States. Plos One, 9(5), e96582.
• Palukaitis, P, Roossinck, MJ, Dietzgen, RG, Francki, RI. 1992. Cucumber mosaic virus. Adv. Virus. Res., 41, 281-348.
• Pérez-de-Castro, A., Martínez de Alba, A.E., Sáez, C., Flores, A., Zifres, A., Gómez-Guillamón, M.L., Lopez, C., Pico, B. 2020. Incidence and genetic diversity of cucurbit viruses in Spain. Acta Hortic,. 1294, 203-210.
• Pozzi, E.A., Bruno, C., Luciani, C.E., Celli, M.G., Conci, V.C., Perotto, M.C. 2020. Relative incidence of cucurbit viruses and relationship with bio-meteorological variables. Australas. Plant Pathol., 49, 167-174.
• Pozzi, E, Perotto, MC, Bertin, S, Manglli, A, Luciani, C, Conci, VC, Tomassoli, L. 2020. Molecular variability of watermelon mosaic virus isolates from Argentina. Eur. J. Plant Pathol., 156(4), 1091-1099.
• Purcifull, D.E., Hiebert, E. 1979. Serological distinction of watermelon mosaic virus isolates. Phytopathology, 69, 112-116.
• Quiot, J. B., Labonne, G., Quiot-Douine, L. 1983. The comparative ecology of cucumber mosaic virus in Mediterranean and tropical regions. In ‘‘Plant Virus Epidemiology’’ (R.T.PlumbandJ.M. Tresh, eds.),pp. 177–183. Blackwell ScientificPublications,Oxford,UK.
• Radouane, N., Ermadi, S., Ezrari, S., Al Figuigui, J., Benjelloune, M., Tahiri, A., Lahlali, R. 2020. Occurrence and distribution of viruses infecting Zucchini and Watermelon in Morocco. Arch. Phytopathol. Plant Prot., 54, 375-387. doi: 10.1080/03235408.2020.1833280.
• Radouane, N., Ezrari, S., Belabess, Z., Tahiri, A., Tahzima, R., Massart, S., Jijakli, H., Benjelloun, M., Lahlali, R. 2021. Viruses of cucurbit crops: current status in the Mediterranean Region. Phytopathol. Mediterr., 60(3), 493-519. doi: 10.36253/phyto-12340.
• Randa-Zelyüt F., Karanfil A., Sarı M., Korkmaz S. 2022. First report of natural infection of wild carrot by Watermelon mosaic virus in Turkey. New Dis. Rep., 46:e12107. https://doi.org/10.1002/ndr2.12107
• Robinson, R.W., Decker-Walter, D.S., 1999. Cucurbits. CAB International Publishing, Cambridge, U.K. Roossinck, M.J. 2002. Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses. J. Virol., 76(7), 3382–3387.
• Roossinck, M.J., Zhang, L., Hellwald, K.H. 1999. Rearrangements in the 5' nontranslated region and phylogenetic analyses of Cucumber mosaic virus RNA 3 indicate radial evolution of three subgroups. J. Virol., 73(8), 6752-6758.
• Sabry, Y.M. Mahmoud 2011. Detection of cucumber mosaic virus in some ornamental plants and elimination of nonspecific ELISA reactions. Arch. Phytopathol. Plant Prot., 44(14), 1410-1424. doi: 10.1080/03235408.2010.505364
• Sacristan, S., Fraile, A., Garcia-Arenal, F. 2004. Population dynamics of Cucumber mosaic virus in melon crops and in weeds in Central Spain. Phytopathology 94:992–998.
• Sharifi, M., Massumi, H., Heydarnejad, J., Pour, A.H., Shaabanian, M., Rahimian. 2008. Analysis of the biological and molecular variability of Watermelon mosaic virus isolates from Iran. Virus Genes. 37: 304-313.
• Srivastava, N., Kapoor, R., Kumar, R., Kumar, S., Saritha, R. K., Kumar, S., Baranwal, V. K. 2019. Rapid diagnosis of Cucumber mosaic virus in banana plants using a fluorescence-based real-time isothermal reverse transcription-recombinase polymerase amplification assay. J. Virol. Methods, 270, 52-58.
• Tan, Z., Wada, Y., Chen, J., Ohshima, K. 2004. Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus. J. Gen. Virol., 85, 2683–2696.
• Usta, M., Güller, A., Günay, A. 2020. The molecular characterization of the coat protein sequence and differentiation of CMV-subgroup I on tobacco from native flora in Turkey. Not. Bot. Horti, Agrobot. Cluj, 48(2), 523-534.
• Wang, D., Li, G. 2017. Host Reaction of Watermelon mosaic virus Isolates Infecting Melon from Different Geographical Origins in Xinjiang of China. Hortic. Plant J., 3, 23–28. doi: 10.1016/j.hpj.2017.01.010.
• Yeşil, S. 2019. Some Virus Diseases of Edible Seed Squash (Cucurbita pepo L.) in Aksaray Province, Turkey. YYU J Agr. Sci., 29(Özel Sayı), 63-71.
• Yuki, V.A., Rezende, J.A.M., Kitajima, E.W., Barroso, P.A.V., Kuniyuki, H., Groppo, G.A., Pavan M.A. (2000). Occurrence, distribution, and relative incidence of five viruses infecting cucurbits in the state of Sao Paulo, Brazil. Plant Dis., 84, 516-520.