İris Bitkilerinde Potyvirüs Enfeksiyonlarının Durumu ve Moleküler Karakterizasyonu: Bilecik İli İris Yetişen Alanlar, Türkiye

Year 2024, , 10 - 17, 03.04.2024

Merve Koç , Filiz Randa Zelyüt

https://doi.org/10.19159/tutad.1342858

Abstract

İris (Iris spp.) bitkilerinde uzun yıllar boyunca yapraklarda şiddetli mozaik, sararma ve nekroz gibi belirtiler gözlemlenmiştir. Bu çalışma kapsamında iris bitkilerinde ilgili simptomlara neden olabilecek Potyvirüs türlerinin varlığı araştırılmıştır. Arazi çalışmaları 2022 yılında Güney Marmara Bölgesi’nde bulunan Bilecik ilinde gerçekleştirilmiştir. Çalışmada, 34 simptomatik ve 7 asimptomatik olmak üzere toplam 41 iris bitkisi toplanmıştır. Potyvirüs enfeksiyonları, Potyvirüs cinsine özgün kısmi NIb (nuclear inclusion protein b) gen bölgesinin amplifikasyonuna yönelik dejenere primerler kullanarak konvansiyonel moleküler yöntemler ile belirlenmiştir. Moleküler çalışmalar sonucunda virüslerin neden olduğu belirtiler gösteren 6 bitkide Potyvirüs enfeksiyonu tespit edilmiştir. Elde edilen 6 Potyvirüs fragmentinin nükleotit dizileme çalışmaları tamamlandıktan sonra enfeksiyonlara iris şiddetli mozaik virüsü (iris severe mosaic virus, ISMV)’nün neden olduğu belirlenmiştir. Bu izolatlar kendi aralarında % 94’ün üzerinde nükleotit benzerliği gösterirken, global izolat ile % 82-99 oranlarında benzerlik göstermiştir. Filogenetik analizler ise bu dejenere primerle elde edilen NIb gen bölgesine göre Potyvirüs türlerinin kendi aralarında başarılı bir şekilde ayrıldığını göstermiştir.

Keywords

Bilecik, iris, Potyvirüs, moleküler karakterizasyon, filogenetik

Status and Molecular Characterization of Potyvirus Infections in Iris Plants: Iris Growing Areas in Bilecik Province, Türkiye

Abstract

Symptoms such as severe mosaic, yellowing and necrosis of leaves have been observed in iris (Iris spp.) plants for many years. In this study, the presence of potyvirus species that can cause similar symptoms in iris plants was investigated. Field surveys were carried out in the province of Bilecik in the South Marmara region-Türkiye in the year 2022. In the study, a total of 41 iris plants were collected, including 34 symptomatic and 7 asymptomatic ones. Potyvirus infections were detected by conventional molecular methods using degenerate primers for amplification of the partial NIb (nuclear inclusion protein b) gene region specific to the genus Potyvirus. As a result of the molecular assays, potyvirus infection was detected in 6 plants showing symptoms caused by viruses. After nucleotide sequencing of the 6 Potyvirus fragments obtained, the infections were determined to be caused by iris severe mosaic virus (ISMV). These isolates showed over 94% nucleotide similarity among themselves and 82-99% similarity with the global isolate. Phylogenetic analyses showed that Potyvirus species were successfully separated among themselves according to the NIb gene region obtained with these degenerate primers.

Keywords

Bilecik, iris, Potyvirus, molecular characterization, phylogenetic

References

• Asjes, C.J., 1979. Viruses and virus diseases in Dutch bulbous irises (Iris hollandica) in the Netherlands. Netherlands Journal of Plant Pathology, 85(6): 269-279.
• Atreya, P.L., Atreya, C.D., Pirone T.P., 1991. Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proceedings of the National Academy of Sciences, 88(17): 7887-7891.
• Brunt, A.A., Phillips, S., 1980. The detection, separation from naturally occurring complexes, and partial characterisation of four aphid-borne viruses infecting bulbous iris. Acta Horticulturae, 109: 503-508.
• Cui, H., Wang, A., 2016. Plum pox virus 6K1 protein is required for viral replication and targets the viral replication complex at the early stage of infection. Journal of Virology, 90(10): 5119-5131.
• Derks, A.F.L.M., 1985. Recent advances in bulb virus research. Acta Horticulturae, 164: 281-289.
• Gibbs, A.J., Hajizadeh, M., Ohshima, K., Jones, R.A.C., 2020. The potyviruses: An evolutionary synthesis is Emerging. Viruses, 12(2): 132.
• Grunwald, D., Stroschein, S.M., Grinstead, S., Mollov, D., Rioux, R.A., Rakotondrafara, A.M., 2023. Targeting the highly conserved 3' untranslated region of Iris severe mosaic virus for sensitive monitoring of the disease prevalence in iris production. Plant Disease, 107(12): 3763-3772.
• Hammond, J., Derks, A.F.L.M., Barnett, O.W., Lawson, R.H., Brunt, A.A., Inouye, N., Allen, T.C., 1985. Viruses infecting bulbous iris: A clarification of nomenclature. Acta Horticulturae, 164: 395-397.
• Inouye, N., Mitsuhata, K., 1978. Turnip mosaic virus isolated from Iris. Nogaku Kenkyu, 57(1): 1-16. (In Japanese).
• Karanfil, A., 2021. Prevalence and molecular characterization of Turkish isolates of the rose viruses. Crop Protection, 143: 105565.
• Karanfil, A., Korkmaz, S., 2022. First report of Iris severe mosaic virus in bulbous irises in Turkey. Journal of Plant Pathology, 104: 859-860.
• Karanfil, A., Randa-Zelyüt, F., Ertunç, F., Korkmaz, S., 2018. First report of rose yellow vein virus in Turkey. New Disease Reports, 38: 11-11.
• Kiliç, H.Ç., Yardimci, N., Gübür, Ş., 2017. Serological, biological and molecular detection of Prunus necrotic ringspot virus on Rosa damascena Mill. in Turkey. Acta Scientiarum Polonorum Hortorum Cultus, 16(1): 145-150.
• Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K., 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547-1549.
• 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.
• 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: 0108277.
• Ohshima, K., Yamaguchi, Y., Hirota, R., Hamamoto, T., Tomimura, K., Tan, Z., Sano, T., Azuhata, F., Walsh, J.A., Fletcher, J., Chen, J., Gera, A., Gibbs, A., 2002. Molecular evolution of turnip mosaic virus: Evidence of host adaptation, genetic recombination and geographical spread. Journal of General Virology, 83(6): 1511-1521.
• Randa-Zelyüt, F., Karanfil, A., Korkmaz, S., 2022. Balıkesir ve Uşak illeri tütün ekim alanlarında potyvirus izolatlarının belirlenmesi ve karakterizasyonu. Çukurova Tarım ve Gıda Bilimleri Dergisi, 37(1): 96-103.
• Revers, F., Garcia, J.A., 2015. Molecular biology of potyviruses. In: K. Maramorosch and T.C. Mettenleiter (Eds.), Advances in Virus Research, Elsevier, 92: 101-199.
• Rodríguez-Nevado, C., Montes, N., Pagán, I., 2017. Ecological factors affecting infection risk and population genetic diversity of a novel Potyvirus in its native wild ecosystem. Frontiers in Plant Science, 8: 1958.
• Tamura, T., 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution, 9(4): 678-687.
• Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22): 4673-4680.
• Valouzi, H., Shahmohammadi, N., Golnaraghi, A., Moosavi, M.R., Ohshima, K., 2022. Genetic diversity and evolutionary analyses of potyviruses infecting narcissus in Iran. Journal of Plant Pathology, 104(1): 237-250.
• Van der Vlugt, C.I.M., 1994. Distribution and multiplication of Iris severe mosaic potyvirus in bulbous Iris in relation to metabolic activity: Implications for ISMV detection. Ph.D. Thesis, Bulb Research Centre Lisse, Dutch Flower bulb Industry, Netherland.
• Wylie, S.J., Adams, M., Chalam, C., Kreuze, J., López-Moya, J.J., Ohshima, K., Praveen, S., Rabenstein, F., Stenger, D., Wang, A., Zerbini, F.M., 2017. ICTV virus taxonomy profile: Potyviridae. Journal of General Virology, 98: 352-354.
• Yardimci, N., Çulal, H., 2009. Occurrence and incidence of Prunus necrotic ringspot virus, Arabis mosaic virus, and Apple mosaic virus on oil rose (Rosa damascena) in the Lakes region of Turkey. New Zealand Journal of Crop and Horticultural Science, 37(2): 95-98.
• Zheng, L., Rodoni, B.C., Gibbs, M.J., Gibbs, A.J., 2010. A novel pair of universal primers for the detection of potyviruses. Plant Pathology, 59(2): 211-220.