New insights into tomato spotted wilt orthotospovirus (TSWV) infections in Türkiye: Molecular detection, phylogenetic analysis, and in silico docking study

Authors

  • Mustafa USTA University of Van Yuzuncu Yil, Faculty of Agriculture, Plant Protection Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba/Van, PK: 65090, Van (TR)
  • Abdullah GÜLLER University of Bingöl, Faculty of Agriculture, Plant Protection Department, Selahaddin-i Eyyubi Mah. Üniversite Cad. No:1, PK: 12000, Bingöl (TR)
  • Serap DEMİREL University of Van Yuzuncu Yil, Faculty of Science, Molecular Biology and Genetic Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba/Van, PK: 65090, Van (TR)
  • Gülüstan KORKMAZ Van Agricultural Resarch Institute, Abdurrahman Gazi Mah. İskele Cad. Çalı Durağı Tuşba/VAN (TR)
  • Zeynelabidin KURT University of Van Yuzuncu Yil, Faculty of Agriculture, Plant Protection Department, Bardakçı, Yüzüncü Yıl Üniversitesi Kampüsü, Tuşba/Van, PK: 65090, Van (TR)

DOI:

https://doi.org/10.15835/nbha51313245

Keywords:

in silico modelling, molecular docking, phylogeny, RT-PCR, TSWV

Abstract

Seventy-eight tomato and pepper plants showing symptoms were tested for tomato spotted wilt orthotospovirus (TSWV) using specific primers targeting the full coat protein gene (CP) through RT-PCR. Plant samples were collected in Denizli region, Türkiye during September 2021. The PCR screening results revealed that 23 samples were infected with TSWV, indicating an infection rate of 29.48%. PCR products were subsequently sequenced bidirectionally, and the obtained sequences were deposited in GenBank under the accession numbers ON323583-84 for pepper, and OQ597214 for tomato. Phylogenetic analysis demonstrated a close relationship between the Turkish-Denizli TSWV isolates and previously reported isolates from tomato and pepper plants in Türkiye (KM407603), Hungary (KJ649612), and Serbia (GU369723). Moreover, in this study, three commercial chemicals and five selected phytochemicals were docked against the TSWV CP to assess their binding energies. The docking results indicate that the tested phytochemicals exhibit promising performance compared to other commercial chemicals. This study represents the first molecular and phylogenetic report on TSWV isolates in pepper and tomato plants in Denizli province, Türkiye. Furthermore, the interaction between TSWV and the selected compounds through in silico docking has been reported for the first time.

References

Abad JA, Moyer JW, Kennedy GG, Holmes GA, Cubeta MA (2005). Tomato spotted wilt virus on potato in eastern North Carolina. American Journal of Potato Research 82:255-261. https://doi.org/10.1007/BF02853592

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

Akdura N, Kılıç HÇ (2022). Hakkari ili domates ve biber üretim alanlarinda yonca mozaik virüsü ve domates lekeli solgunluk virüsü’nün belirlenmesi [Detection of alfalfa mosaic virus and tomato spotted wilt virus in tomato and pepper growing areas of Hakkari province]. Süleyman Demirel University Journal of Natural and Applied Sciences 26(3):435-440. https://doi.org/10.19113/sdufenbed.1082948

An M, Zhou T, Guo Y, Zhao X, Wu Y (2019). Molecular regulation of host defense responses mediated by biological anti-TMV agent Ningnanmycin. Viruses 11(9):815. https://doi.org/10.3390/v11090815

Aranda M, Maule A (1998). Virus-induced host gene shutoff in animals and plants. Virology 243(2):261-267. https://doi.org/10.1006/viro.1998.9032

Arli-Sokmen M, Menna H, Sevik MA, Ecevit O (2005). Occurrence of viruses in field-grown pepper crops and some of their reservoir weed hosts in Samsun, Turkey. Phytoparasitica 33:347-358. https://doi.org/10.1007/BF02981301

Arli-Sokmen M, Sevik MA (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

Azeri T (1994). Detection of Tomato spotted wilt virus in tobacco and tomato cultivars by ELISA. Journal Turkish Phytopathology 23(1):37-46.

Beşkeçili M, Güneş N, Gümüş M (2021). Antalya ili Demre ilçesi biber yetiştiriciliğinde tomato spotted wilt virus (TSWV) ve Cucumber mosaic virus (CMV) etmenlerinin yaygınlığının belirlenmesi [Determination and prevalence of Tomato spotted wilt virus (TSWV) and Cucumber mosaic virus (CMV) in pepper production areas in Demre district of Antalya]. Journal of Agriculture Faculty of Ege University 58(3):399-405. https://doi.org/10.20289/zfdergi.799432

Brittlebank CC (1919). Tomato diseases. Journal of Agriculture Victoria 17:231-235.

Chiemsombat P, Adkins S (2006). Tospoviruses. In: Rao GP, Lava Kumar P, Holguín-Peña RJ (Eds). Characterization, diagnosis and management of plant viruses. Studium Press, Houston, Spain pp 1-37.

Değirmenci K, Uzunoğulları N (2007). Determination of problem viruses on the tomatoes cultivation areas in Marmara Region. Plant Protection Bulletin 47:72-77.

Demirel S, Usta M, Güller A (2022). In silico analysis of ribosome-inactivating protein (tritin) from common wheat plants (Triticum aestivum L.). European Journal of Science and Technology 33:79-87. https://doi.org/10.31590/ejosat.1021686

Devjani C, Sunanda C (2010). Bioassay-guided isolation and identification of antibacterial and antifungal component from methanolic extract of green tea leaves (Camellia sinensis). Research Journal of Phytochemistry 4(2):78-86.

Ertunç F (2020). Physiology of virus-infected plants. In: Awasthi LP (Ed). Applied Plant Virology. Academic Press, pp 199-205. https://doi.org/10.1016/B978-0-12-818654-1.00015-3

Foissac L, Gentit P, Svanetia-Dumas L, Dulucq MJ, 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 Horticulturae 550:37- 43. https://doi.org/10.17660/ActaHortic.2001.550.2

Gao S, Wu J (2022). Detection of tomato spotted wilt virus (TSWV) infection in plants using DAS-ELISA and dot-ELISA. In: Wang A, Li Y (Eds). Plant Virology. Methods in Molecular Biology. Humana, New York pp 253-261. https://doi.org/10.1007/978-1-0716-1835-6_24

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research 31(13):3784-3788. https://doi.org/10.1093/nar/gkg563

Geyik S (2017). Investigation on tomato virüs diseases of virüs in tomato growing areas in the Marmara region of Turkey. MSc Dissertation, Namık Kemal University, Tekirdağ, Türkiye.

Gitaitis RD, Dowler CC, Chalfant RB (1998). Epidemiology of Tomato spotted wilt virus in pepper and tomato in Southern Georgia. Plant Disease 82:752-756. https://doi.org/10.1094/PDIS.1998.82.7.752

Goldbach R, Peters D (1994). Possible causes of the emergence of tospovirus diseases. Seminars in Virology 5(2):113-120. https://doi.org/10.1006/smvy.1994.1012

Güneş N, Gümüş M (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

Hari V, Das P (1998). Ultra microscopic detection of plant viruses and their gene products. In: Hadidi A, Khetarpal RK, Koganezawa H (Eds). Plant Disease Virus Control, APS Press, St. Paul pp 417-427.

Jankowski F, Slawinski FA, Mazur M, Micinski B, Wegorek W (1980). The economic importance of the TSWV in tobacco growing and the results of control of the vector of this disease the tobacco thrips Thrips tabaci Lind. Page 279. In: Proc. XIX Conf. Scient. Inst. Plant Protect., 1979: Materialy XIX Sesji Naukowej Instytutu Ochrony, Roslin.

Kikkert M, Verschoor A, Kormerlink R, Rottier P, Goldbach R (2001). Tomato spotted wilt virus glycoproteins exhibit trafficking and localization signals that are functional in mammalian cells. Journal of Virology 75(2):1004-1012. https://doi.org/10.1128/jvi.75.2.1004-1012.2001

Kılıç HÇ, Isparta L, Yardımcı N, Doğan K (2017). Diagnosis of Tomato spotted wilt virus (TSWV) in tomatoes grown areas in Isparta and Burdur provinces, Turkey. The Journal of Graduate School of Natural and Applied Sciences of Mehmet Akif Ersoy University 8(1):34-39. https://doi.org/10.29048/makufebed.261783

Küçük B, Kamberoglu M (2008). Detection of tomato spotted wilt virus (TSWV) in Adana and Mersin provinces and biological characterization of some TSWV isolates. Çukurova Journal of Agriculture and Food Sciences 23:17- 24.

Laliberté JF, Zheng H (2014). Viral manipulation of plant host membranes. Annual Review of Virology 1:237-259. https://doi.org/10.1146/annurev-virology-031413-085532

Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26(2):283-291. https://doi.org/10.1107/S0021889892009944

Li X, Hao G, Wang Q, Chen Z, Ding Y, Yu L, ... Song B (2017). Ningnanmycin inhibits tobacco mosaic virus virulence by binding directly to its coat protein discs. Oncotarget 8(47):82446. https://doi.org/10.18632%2Foncotarget.19401

Mandal B, Mandal S, Csinos AS, Martinez N, Culbreath AK, Pappu HR (2008). Biological and molecular analyses of the acibenzolar- S-methylinduced systemic acquired resistance in flue-cured tobacco against Tomato spotted wilt virus. Phytopathology 98:96-204. https://doi.org/10.1094/PHYTO-98-2-0196

Morca AF, Çelik A, Coşkan S, Santosa AI, Akbaş B (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 118:101786. https://doi.org/10.1016/j.pmpp.2022.101786

Morozova ON, Zvyagintseva DD, Beloshapkina OO (2021). Laboratory diagnostics of tomato spotted wilt virus by PCR. bioRxiv, 2021-01. https://doi.org/10.1101/2021.01.17.426990

Mumford R, Macarthur R, Boonham N (2016). The role and challenges of new diagnostic technology in plant biosecurity. Food Security 8:103-109. https://doi.org/10.1007/s12571-015-0533-y

NCBI (2023). National Center for Biotechnology Information. Retrieved 2023 April 15 from https://www.ncbi.nlm.nih.gov

Oana D, Erdei L, Vidacs Livia DM, Baciu Anca DI, Berbentea F (2009). Influence of ribavirin on potato plants regeneration and virus eradication. Journal of Horticulture, Forestry and Biotechnology 13:421-425.

Özdemir S, Erilmez S, Kaçan K (2009). Detection of Tomato spotted wilt virus (TSWV) on tomato crops and some weeds in Denizli province of Turkey. In: II. International Symposium on Tomato Diseases. Türkiye pp 171-174.

Pappu HR (2008). Tomato spotted wilt virus. In: Mahy BWJ, Regenmortel MHV (Eds). Encyclopedia of Virology. Academic press, Oxford, UK pp 133-138. https://doi.org/10.1016/B978-012374410-4.00648-8

Pappu HR, Jones RAC, Jain RK (2009). Global status of tospovirus epidemics in diverse cropping systems: Successes gained and challenges that lie ahead. Virus Research 141:219-236. https://doi.org/10.1016/j.virusres.2009.01.009

Pataky NR (1991). Tomato spotted wilt virus, report on Plant Disease. Department of Crop Sciences, University of Illinois, Urbana-Champaign.

Paunovic S, Ruzic D, Vujovic T, Milenkovic S, Jevremovic D (2007). In vitro production of Plum pox virus-free plums by chemotherapy with ribavirin. Biotechnology and Biotechnological Equipment 21(4):417-421. https://doi.org/10.1080/13102818.2007.10817486

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25(13):1605-1612. https://doi.org/10.1002/jcc.20084

Quecini V, Lopes ML, Pacheco FT, Ongarelli MDG (2008). Ribavirin, a guanosine analogue mammalian antiviral agent, impairs tomato spotted wilt virus multiplication in tobacco cell cultures. Archives of Phytopathology and Plant Protection 41(1):1-13. https://doi.org/10.1080/03235400600628047

Rosello S, Diez MJ, Nuez F (1996). Viral diseases causing the greatest economic losses to the tomato crop. I. The Tomato spotted wilt virus -a review. Scienta Horticulturae 67:117-150. https://doi.org/10.1016/S0304-4238(96)00945-4

Santamaria-Hernando S, Senovilla M, González-Mula A, Martínez-García PM, Nebreda S, Rodríguez-Palenzuela P, ... Rodríguez-Herva JJ (2019). The Pseudomonas syringae pv. tomato DC3000 PSPTO_0820 multidrug transporter is involved in resistance to plant antimicrobials and bacterial survival during tomato plant infection. PLoS One 14(6):e0218815. https://doi.org/10.1371/journal.pone.0218815

Scholthof KBG, Adkins S, Czosnek H, Palukaitis P, Jacquot E, Hohn T, ... Foster GD (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

Sertkaya G, Yılmaz M (2017). Hatay ili örtüalti organik domates yetiştiriciliğinde bazi begomovirüslerin enfeksiyon oranlari ile doğal taşinmasi ve diğer konukçularinin araştirilmasi [Investigation on some begomoviruses, their natural transmission and other hosts in organic tomato production in greenhouses in Hatay province of Turkey]. Journal of Agricultural Faculty of Mustafa Kemal University 22(1):1-15.

Severson WE, Schmaljohn CS, Javadian A, Jonsson CB (2003). Ribavirin causes error catastrophe during Hantaan virus replication. Journal of Virology 77(1):481-488. https://doi.org/10.1128/jvi.77.1.481-488.2003

Shabana YM, Abdalla ME, Shahin AA, El-Sawy MM, Draz IS, Youssif AW (2017). Efficacy of plant extracts in controlling wheat leaf rust disease caused by Puccinia triticina. Egyptian Journal of Basic and Applied Sciences 4(1):67-73. https://doi.org/10.1016/j.ejbas.2016.09.002

Sherman JM, Moyer JW, Daub ME (1998). Tomato spotted wilt virus resistance in chrysanthemum expressing the viral nucleocapsid gene. Plant Disease 82(4):407-414. https://doi.org/10.1094/PDIS.1998.82.4.407

Sidwell RW, Huffman JH, Khare Lois GP, Allen B, Witkowski Roland JT, Robins K (1972). Broad-spectrum antiviral activity of virazole: 1-β-D-ribofuranosyl-1, 2, 4-triazole-3-carboxamide. Science 177(4050):705-706. https://doi.org/10.1126/science.177.4050.705

Şin B (2015). Characterizaiton of tomato spotted wilt virus (TSWV) isolates causing infection in tomato fields in Amasya, Samsun and Tokat provinces. MSc Dissertation, Ondokuz Mayıs University, Samsun, Türkiye.

Stange C (2006). Plant-virus interactions during the infective process. Ciencia Investigacion Agraria 33(1):1-18.

Tekinel N, Dolar MS, Sağsöz S, Salcan Y (1969). Mersin Bölgesinde ekonomik bakımdan önemli bazı sebzelerin virüsleri üzerinde araştırmalar [Researches on viruses of some economically important vegetables in Mersin Region]. Plant Protection Bulletin 9(1):37-49.

Topkaya Ş (2021). Prevalence and molecular characterization of tomato spotted wilt virus in pepper fields in Tokat province. Plant Protection Bulletin 61(3):28-35. https://doi.org/10.16955/bitkorb.898371

Tsompana M, Moyer JW (2008). Tospovirus. In: Mahy BWJ, Regenmortel MHV (Eds). Encyclopedia of virology. Academic Press, pp 157-163. https://doi.org/10.1016/B978-012374410-4.00517-3

Turhan P, Korkmaz S (2006). Determination of tomato spotted wilt virus using serological and biological methods in tomatoes grown in Çanakkale province. Journal of Agricultural Sciences 12(2):130-137.

Ullman DE, German TL, Sherwood JL, Westcot DM, Cantone FA (1993). Tospovirus replication in insect vector cells: immunocytochemical evidence that the nonstructural protein encoded by the S RNA of tomato spotted wilt tospovirus is present in thrips vector cells. Phytopathology 83:456-463.

Wang Z, Feng A, Cui M, Liu Y, Wang L, Wang Q (2012). First discovery and stucture-activity relationship study of phenanthroquinolizidines as novel antiviral agents against tobacco mosaic virus (TMV). PLoS One 7(12):e52933. https://doi.org/10.1371/journal.pone.0052933

Wangai AW, Mandal B, Pappu H, Kilonzo S (2001). Outbreak of Tomato spotted wilt virus in tomato in Kenya. Plant Disease 85:1123. https://doi.org/10.1094/PDIS.2001.85.10.1123B

Wells ML, Culbreath AK, Todd JW, Brown SL, Gorbet DW (2002). A regression approach for comparing field resistance of peanut cultivars to tomato spotted wilt tospovirus. Crop Protection 21(6):467-474.

Wilson CR (1998). Incidence of weed reservoirs and vectors of Tomato spotted wilt tospovirus on southern Tasmanian lettuce farms. Plant Pathology 47:171-176. https://doi.org/10.1046/j.1365-3059.1998.00227.x

Yang JQ, Song BA, Bhadury PS, Chen Z, Yang S, Cai XJ, ... Xue W (2010). Synthesis and antiviral bioactivities of 2-cyano-3-substituted-amino (phenyl) methylphosphonylacrylates (acrylamides) containing alkoxyethyl moieties. Journal of Agricultural and Food Chemistry 58(5):2730-2735. https://doi.org/10.1021/jf902861m

Yardımcı N, Çulal-Kılıç H (2009). Tomato spotted wilt virus in vegetable growing areas in the west mediterranean region of Turkey. African Journal of Biotechnology 8(18):4539-4541.

Yeşil S (2022). Serological Detection of Three Common Tomato Viruses in Tomato Cultivation Areas of Ereğli District, Konya. Turkish Journal of Agriculture-Food Science and Technology 10:2795-2800. https://doi.org/10.24925/turjaf.v10isp1.2795-2800.5746

Yılmaz E (2014). Investigations ontheidentification of virus diseases in the vegetable growing areas of Edirne province in Turkey. MSc Dissertation, Namık Kemal University, Tekirdağ, Türkiye.

Zarzyńska-Nowak A, Hasiów-Jaroszewska B, Korbecka-Glinka G, Przybyś M, Borodynko-Filas N (2018). A multiplex RT-PCR assay for simultaneous detection of tomato spotted wilt virus and tomato yellow ring virus in tomato plants. Canadian Journal of Plant Pathology 40(4):580-586. https://doi.org/10.1080/07060661.2018.1503195

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2023-09-04

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USTA, M., GÜLLER, A., DEMİREL, S., KORKMAZ, G., & KURT, Z. (2023). New insights into tomato spotted wilt orthotospovirus (TSWV) infections in Türkiye: Molecular detection, phylogenetic analysis, and in silico docking study. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(3), 13245. https://doi.org/10.15835/nbha51313245

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Vol. 51 No. 3 (2023)

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Research Articles
CITATION
DOI: 10.15835/nbha51313245

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