Evaluation of genetic diversity of tomato spotted wilt virus (TSWV) NSs gene region isolates at geographical level

Abstract

One of the most significant plant protection problems that adversely affect agricultural production is diseases caused by viruses, as there are no direct and rapid control methods. Tomato spotted wilt virus (TSWV), which is known to cause major losses in vegetable production and is quite common in the Mediterranean basin, is one of these viruses. In reducing the prevalence of the agent, control of vector insects and use of resistant varieties are the primary parameters. In this study, the genetic diversity of the partial Non-Structural NSs gene, which produces a putative silencing suppressor protein of TSWV, was investigated at the level of geographical populations. A total of 325 isolates were clustered from Eastern European, European Mediterranean, Asian, African, and American populations and geographic genetic diversity analyses were performed. Phylogenetic analyses revealed 2 major phylogroups (Clade I and II). Isolates reported from Asia and Africa were clustered only in Clade II, while other isolates were distributed in both groups. Haplotype network analyses revealed that the isolates had genotypes partially related to their geography. In support of these results, molecular variance analyses (AMOVA) showed that there were significant results for both proposals when applied between and within geographic groups. The findings highlight that TSWV has experienced different evolutionary processes in geographical regions, that the virus spreads along different genetic lines in regions, that local genotypes may dominate in regions and potentially adapt more quickly, and that local plant health institutions should increase regional quarantine measures and isolation strategies, and that it is important to take these genetic differences into account in order for the control to be more effective and targeted.

Keywords

• TSWV
• NSs gene
• haplotype network
• AMOVA

References

1. Abadkhah M, Koolivand D, Eini O. 2018. A new distinct clade for Iranian Tomato spotted wilt virus isolates based on the polymerase, nucleocapsid, and non-structural genes. Plant Pathol J. 34:514.
2. Almási A, Csilléry G, Csömör Z, et al. 2015. Phylogenetic analysis of Tomato spotted wilt virus (TSWV) NSs protein demonstrates the isolated emergence of resistance-breaking strains in pepper. Virus Genes. 50:71–78.
3. Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37-48. doi: 10.1093/oxfordjournals.molbev.a026036.
4. De Haan P, Kormelink R, de Oliveira Resende R, van Poelwijk F, Peters D, Goldbach R. 1991. Tomato spotted wilt virus L RNA encodes a putative RNA polymerase. J Gen Virol. 71:2207–2216.
5. De Ronde D, Butterbach P, Lohuis D, Hedil M, Van Lent JW, Kormelink R. 2013. Tsw gene-based resistance is triggered by a functional RNA silencing suppressor protein of the Tomato spotted wilt virus. Mol Plant Pathol. 14:405–415. doi: 10.1111/mpp.12016
6. Du J, Song XY, Shi XB, Tang X, Chen JB, Zhang ZH, Chen G, Zhang Z, Zhou XG, Liu Y, Zhang DY. 2020. NSs, the Silencing Suppressor of Tomato Spotted Wilt Orthotospovirus, Interferes With JA-Regulated Host Terpenoids Expression to Attract Frankliniella occidentalis. Front Microbiol. 11:590451.doi: 10.3389/fmicb.2020.590451.
7. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131:479-491.
8. Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10:564-567.

9. Francki RIB, Hatta T. 1981. Tomato spotted wilt virus. In:Kurstak E, ed. Handbook of Plant Virus Infections andComparative Diagnosis. Amsterdam: Elsevier/North Hol-land Biomedical Press. 492–511.
10. Guo Y, Liu B, Ding Z, Li G, Liu M, Zhu D, Sun Y, Dong S, Lou Z. 2017. Distinct mechanism for the formation of the ribonucleoprotein complex of Tomato spotted wilt virus. J Virol. 91:e00892-17.
11. Gupta R, Kwon SY, Kim ST. 2018 An insight into the tomato spotted wilt virus (TSWV), tomato and thrips interaction. Plant Biotechnol Rep. 12:157–163.
12. Güller A, Usta M, Randa-Zelyüt F. 2023. Genetic diversity and population structure of tomato brown rugose fruit virus (ToBRFV) variants from Antalya province, Turkey. Notulae Botanicae Horti Agrobotanici Cluj-Napoca. 51:13356-13356.
13. Jones L. 1944. Streak and mosaic of Cineraria. Phytopathology. 34:941–953.
14. Kamran A, Li Y, Zhang W, Jiao Y, Farooq T, Wang Y, Liu D, Jiang L, Shen L, Wang F, Yang J. 2024. Insights into the genetic variability and evolutionary dynamics of tomato spotted wilt orthotospovirus in China. BMC Genomics. 8:40. doi: 10.1186/s12864-023-09951-9.
15. Karanfil A, Randa-Zelyüt F, Korkmaz S. 2023. Population structure and genetic diversity of tobacco mild green mosaic virus variants in Western Anatolia of Turkey. Physiol Mol Plant Pathol. 125:102008.
16. Leigh JW, Bryant D. 2015. POPART: full-feature software for haplotype network construction. Methods Ecol Evol. 6:9.
17. Letunic I, Bork P. 2024. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. gkae268. doi: 10.1093/nar/gkae268
18. Margaria P, Bosco L, Vallino M, Ciuffo M, Mautino GC, Tavella L, Turina M. 2014. The NSs protein of tomato spotted wilt virus is required for persistent infection and transmission by Frankliniella occidentalis. J Virol. 88:5788-802. doi: 10.1128/JVI.00079-14.
19. 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. Physiol Mol Plant Pathol. 118:101786.
20. Nagata T, Inoue-Nagata AK, Prins M, Goldbach R, Peters D. 2000. Impeded thrips transmission of defective Tomato spotted wilt virus isolates. Phytopathology. 90:454–459.
21. Ocampo TO, Peralta SMG, Bacheller N, Uiterwaal S, Knapp A, Hennen A, Ochoa-Martinez DL, Garcia-Ruiz H. 2016. Antiviral RNA silencing suppression activity of Tomato spotted wilt virus NSs protein. Genet Mol Res. 15:15028625.
22. Oetting RD. 1991. The effect of host species and different plant components on thrips feeding and development. In: Hsu TH, Lawson HR (eds) Virus–Thrips–Plant Interactionof Tomato Spotted Wilt Virus. United States Department Agriculture Research and Service. Maryland, pp 15–20.
23. Peiró A, Cañizares MC, Rubio L, López C, Moriones E, et al. 2014. The movement protein (NSm) of tomato spotted wilt virus is the avirulence determinant in the tomato Sw‐5 gene‐based resistance. Mol Plant Pathol. 15:802-813. https:// doi.org/10.1111/mpp.12142
24. Prins M, Goldbach R. 1998 The emerging problem of tospovirus infection and nonconventional methods of control. Trends Microbiol. 6:31–35
25. Reitz SR, Gao Y, Kirk WDJ, Hoddle MS, Leiss KA, Funderburk JE. 2020. Invasion Biology, Ecology, and management of Western Flower Thrips. Annu Rev Entomol. 65:17–37.
26. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34:3299-3302.
27. Santosa AI, Randa-Zelyüt F, Karanfil A, et al. 2023. Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N. Virus Genes. 59:121–131.
28. Snippe M, Borst JW, Goldbach R, Kormelink R. 2007. Tomato spotted wilt virus Gc and N proteins interact in vivo. Virology. 357:115–123.
29. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 10:512–526.
30. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 38:3022-3027.
31. Turina M, Tavella L, Ciuffo M. 2012. Tospoviruses in the Mediterranean area. Advances in Virus Research. 84:403-437.
32. Turina M, Kormelink R, Resende RO. 2016. Resistance to tospoviruses in vegetable crops: epidemiological and molecular aspects. Annu Rev Phytopathol. 54: 347-371. https:// doi.org/10.1146/annurev-phyto-080615-095843
33. Usta M, Güller A, Demirel 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, Not Bot Horti Agrobot Cluj-Napoca. 51:1–22.
34. Wang H, Wu X, Huang X, Wei S, Lu Z, Ye J. 2022. Seed Transmission of Tomato Spotted Wilt Orthotospovirus in Peppers. Viruses. 14:1873. doi: 10.3390/v14091873.
35. Whitfield AE, Kumar NKK, Rotenberg D, Ullman DE, Wyman EA, Zietlow C, Willis DK, German TL (2008) A soluble form of the Tomato spotted wilt virus (TSWV) glycoprotein G(N) (G(N)-S) inhibits transmission of TSWV by Frankliniella occidentalis. Phytopathology. 98:45–50.
36. Zelyüt FR, Ertunç F. 2021. Population genetic analysis of lettuce big-vein disease viruses and their vector fungi Olpidium virulentus in Ankara province, Turkey. Physiol Mol Plant Pathol. 113:101593.