Research Article
Çanakkale İlinde Leek yellow stripe virus Enfeksiyonunun Güncel Durumu ve İki farklı Gen Bölgesine Göre Kısmi Moleküler Karakterizasyonu
Abstract
Pırasa sarı çizgi virüsü (Leek yellow stripe virus, LYSV) pırasa tarımında ekonomik kayıplara neden olan en önemli viral hastalık etmenlerinden birisidir. Ülkemizin farklı illeri ve bölgelerinden LYSV’nin varlığı bugüne kadar yapılan birçok çalışmada bildirilmiştir. Ancak, yapılan bu çalışmalar virüsün tespiti ve kılıf protein (Coat Protein; CP) geninin moleküler karakterizasyonuna yöneliktir. Ayrıca etmenin enfeksiyonu yıldan yıla değişkenlik gösterebilmektedir. Bu nedenlerle virüsün güncel enfeksiyon durumun belirlenmesi ve iki farklı gen bölgesine göre virüsün kısmi moleküler karakterizasyonunun yapılması amacıyla bu çalışma planlanmıştır. Bu amaçla, 2019 yılında Çanakkale’nin 3 ilçesinde (Merkez, Ezine ve Ayvacık) arazi çalışmaları yapılarak virüs ve virüs benzeri belirti gösteren 35 pırasa bitkilerinden örnekler alınmıştır. Alınan örnekler double antibody sandwich-enzyme-linked immunosorbent assay (DAS-ELISA) ile LYSV varlığı açısından testlenmiş ve 32 tanesinin enfekteli olduğu bulunmuştur. Enfekteli bulunan örnekler içerisinden 2, daha önce yapılan bir çalışmadan (Korkmaz ve Çevik, 2009) elde edilen örneklerden de 2 tane olmak üzere toplam 4 örneğin nüklear inclusion b (Nuclear Inclusion b; NIb) ve CP gen bölgesi çoğaltılıp dizilenerek kısmi moleküler karakterizasyonu gerçekleştirilmiştir. Yapılan çoklu dizi analizleri sonucunda Çanakkale LYSV izolatlarının her iki gen bölgesine göre de birbirleri ile %90’ın üzerinde dizi benzerliği gösterdiği tespit edilmiştir. Filogenetik analizler sonucunda ise özellikle NIb bölgesine göre Çanakkale LYSV izolatlarının birbirleri ile yakın ilişkili olduğu belirlenmiştir
Keywords
Supporting Institution
TÜBİTAK
Project Number
2209-A
References
- Bampi, D., Mituti, T., Pavan, M. A., Hammond, J. ve Krause-Sakate, R. (2015). Leek yellow stripe virus isolates from Brazil form a distinct clade based on the P1 gene. Journal of Plant Pathology, 97(3), 457-463. https://www.researchgate.net/publication/292816896_Leek_yellow_stripe_virus_isolates_from_Brazil_form_a_distinct_clade_based_on_the_P1_gene.
- Barg, E., Lesemann, D. E., Vetten, H. J. ve Green, S. K. (1993). Identification, partial characterization, and distribution of viruses infecting Allium crops in South and Southeast Asia. In International Symposium on Alliums for the Tropics, 358, 251-258. https://doi.org/10.17660/ActaHortic.1994.358.41 Clark, M.F. ve Adams, A.N. (1977). Characteristic of the Microplate Method of Enzyme Linked Immune Sorbent Assay for the Detection of Plant Viruses. Journal of General Virology, 34(3), 475-483. https://doi.org/10.1099/0022-1317-34-3-475
- Conci, V. C., Lunello, P., Buraschi, D., Italia, R. R., & Nome, S. F. (2002). Variations of Leek yellow stripe virus concentration in garlic and its incidence in Argentina. Plant Disease, 86(10), 1085-1088. https://doi.org/10.1094/PDIS.2002.86.10.1085
- Davis, P.H., (1984). Flora of Turkey and the East Aegeon Islands. Vol.8, Edinburgh, Univ. Press, Edinburgh.
- Dovas, C.I., Hatziloukas, E., Salomon, R., Barg, E., Shiboleth, Y. ve Katis N.I. (2001). Incidence of viruses infecting Allium spp. in Greece. European Journal of Plant Pathology, 107(7), 677-684. https://doi.org/10.1023/A:1011958914573
- Dovas, C.I., Hatziloukas, E., Salomon, R., Barg, E., Shiboleth, Y. ve Katis, N.I. (2002). Comparisons of Methods For Virus Detection in Allium spp. Journal of Phytopathology, 149(11-12), 11-12. https://doi.org/10.1046/j.1439-0434.2001.00705.x
- Fidan, H. ve Baloglu, S. (2009). First report of leek yellow stripe virus on leek in Turkey. Journal of Plant Pathology, 91(1), 234. https://www.researchgate.net/publication/290102219_First_report_of_Leek_yellow_stripe_virus_on_leek_in_Turkey
- Fidan, H. (2010). Sarımsak, Soğan ve Pırasa’daki Virüs Hastalıklarının Saptanması ve Taşköprü 56 Sarımsak Tipinin En Yaygın Virüse Karşı Reaksiyonunun Belirlenmesi (Doktora Tezi). Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Korkmaz, S. ve Cevik, B. (2009). Leek yellow stripe virus newly reported in Turkey. Plant Pathology, 58(4), 787. 10.1111/j.1365-3059.2009.02049.x
- Kurtuluş, E., (2012). Çanakkale İlinde Pırasa Sarı Çizgi Virüsü (Leek Yellow Stripe Virus; LYSV)’nün Biyolojik ve Moleküler Karakterizasyonu (Yüksek Lisans Tezi) Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J. ve 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. https://doi.org/10.1016/j.jviromet.2008.09.008
- Lunello, P., Ducasse, D. ve Conci, V. (2005). Improved PCR Detection of Potyviruses in Allium Species. European Journal of Plant Pathology, 112(4):371-378. https://doi.org/10.1007/s10658-005-6232-3
- Mertens, P. P. C., Maan, S., Samuel, A., Attoui, H., Fauquet, C. M., Mayo, M. A. et al. (2005). Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. Fauquet, 447-454.
- Muhire, B.M., Varsani, A. ve Martin, D.P. (2014). SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One, 9, 0108277. https://doi.org/10.1371/journal.pone.0108277
- Pappu, H.R., Hellier, B.C. ve Dugan, F.M. (2005). First report of Onion yellow dwarf virus, Leek yellow stripe virus, and Garlic common latent virus in garlic in Washington State. Plant Disease, 89(2), 205-205. https://doi.org/10.1094/PD-89-0205C
- Takaki, F., Sano, T., Yamashita, K., Fujita, T., Ueda, K., ve Kato, T. (2005). Complete nucleotide sequences of attenuated and severe isolates of Leek yellow stripe virus from garlic in northern Japan: Identification of three distinct virus types in garlic and leek world-wide. Archives of Virology, 150(6), 1135-1149. https://doi.org/10.1007/s00705-004-0482-9
- Tuzlalı, H.T. (2018). Güney Marmara Bölgesi’nde Allıum Cinsi Bitkilerde Potyvirüslerin Tanılanması ve Karakterizasyonu (Doktora Tezi). Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Wylie, S. J., Adams, M., Chalam, C., Kreuze, J., López-Moya, J. J., Ohshima, K. et al. (2017). ICTV virus taxonomy profile: Potyviridae. Journal of General Virology, 98(3), 352. https://doi.org/10.1099/jgv.0.000740
- Zheng, L., Rodoni, B. C., Gibbs, M. J. ve Gibbs, A. J. (2010). A novel pair of universal primers for the detection of potyviruses. Plant Pathology, 59(2), 211-220. https://doi.org/10.1111/j.1365-3059.2009.02201.x
Current Status of Leek yellow stripe virus in Çanakkale Province of Turkey and Partial Molecular Characterization of Turkish Isolates Based on Two Gene Regions
Abstract
Leek yellow stripe virus (LYSV) is one of the most important viral disease agents causing economic losses in leek cultivation. The presence of this virus has been previously reported in different provinces and regions of Turkey. However, those studies to date in Turkey were limited to the detection of LYSV and characterization the coat protein (CP) gene of LYSV isolates. Moreover, the infection rate of LYSV may vary from year to year. Therefore, this study was initiated to determine the current infection situation of LYSV in Çanakkale province, Turkey and partial molecular characterization of the virus based on two different genomic regions. For those purposes, field studies were conducted in 3 districts of Çanakkale province (Merkez, Ezine and Ayvacık), and 35 leek plants showing virus-like symptoms were sampled in 2019. The samples were tested with double antibody sandwich-enzyme-linked immunosorbent (DAS-ELISA) assay for the presence of LYSV and 32 of 35 collected samples were infected with LYSV. The nuclear inclusion b (NIb) and the CP genes of two new and two 2 previously obtained isolates (Korkmaz and Cevik, 2009) were amplified and sequenced for partial molecular characterization. Multiple sequence alignment studies showed that Çanakkale LSYV isolates have over %90 sequence identities with each other based on two genomic regions. Moreover, phylogenetic analysis revealed that Çanakkale LYSV isolates are closely related to each other especially based on NIb region.
Keywords
Project Number
2209-A
References
- Bampi, D., Mituti, T., Pavan, M. A., Hammond, J. ve Krause-Sakate, R. (2015). Leek yellow stripe virus isolates from Brazil form a distinct clade based on the P1 gene. Journal of Plant Pathology, 97(3), 457-463. https://www.researchgate.net/publication/292816896_Leek_yellow_stripe_virus_isolates_from_Brazil_form_a_distinct_clade_based_on_the_P1_gene.
- Barg, E., Lesemann, D. E., Vetten, H. J. ve Green, S. K. (1993). Identification, partial characterization, and distribution of viruses infecting Allium crops in South and Southeast Asia. In International Symposium on Alliums for the Tropics, 358, 251-258. https://doi.org/10.17660/ActaHortic.1994.358.41 Clark, M.F. ve Adams, A.N. (1977). Characteristic of the Microplate Method of Enzyme Linked Immune Sorbent Assay for the Detection of Plant Viruses. Journal of General Virology, 34(3), 475-483. https://doi.org/10.1099/0022-1317-34-3-475
- Conci, V. C., Lunello, P., Buraschi, D., Italia, R. R., & Nome, S. F. (2002). Variations of Leek yellow stripe virus concentration in garlic and its incidence in Argentina. Plant Disease, 86(10), 1085-1088. https://doi.org/10.1094/PDIS.2002.86.10.1085
- Davis, P.H., (1984). Flora of Turkey and the East Aegeon Islands. Vol.8, Edinburgh, Univ. Press, Edinburgh.
- Dovas, C.I., Hatziloukas, E., Salomon, R., Barg, E., Shiboleth, Y. ve Katis N.I. (2001). Incidence of viruses infecting Allium spp. in Greece. European Journal of Plant Pathology, 107(7), 677-684. https://doi.org/10.1023/A:1011958914573
- Dovas, C.I., Hatziloukas, E., Salomon, R., Barg, E., Shiboleth, Y. ve Katis, N.I. (2002). Comparisons of Methods For Virus Detection in Allium spp. Journal of Phytopathology, 149(11-12), 11-12. https://doi.org/10.1046/j.1439-0434.2001.00705.x
- Fidan, H. ve Baloglu, S. (2009). First report of leek yellow stripe virus on leek in Turkey. Journal of Plant Pathology, 91(1), 234. https://www.researchgate.net/publication/290102219_First_report_of_Leek_yellow_stripe_virus_on_leek_in_Turkey
- Fidan, H. (2010). Sarımsak, Soğan ve Pırasa’daki Virüs Hastalıklarının Saptanması ve Taşköprü 56 Sarımsak Tipinin En Yaygın Virüse Karşı Reaksiyonunun Belirlenmesi (Doktora Tezi). Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Korkmaz, S. ve Cevik, B. (2009). Leek yellow stripe virus newly reported in Turkey. Plant Pathology, 58(4), 787. 10.1111/j.1365-3059.2009.02049.x
- Kurtuluş, E., (2012). Çanakkale İlinde Pırasa Sarı Çizgi Virüsü (Leek Yellow Stripe Virus; LYSV)’nün Biyolojik ve Moleküler Karakterizasyonu (Yüksek Lisans Tezi) Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J. ve 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. https://doi.org/10.1016/j.jviromet.2008.09.008
- Lunello, P., Ducasse, D. ve Conci, V. (2005). Improved PCR Detection of Potyviruses in Allium Species. European Journal of Plant Pathology, 112(4):371-378. https://doi.org/10.1007/s10658-005-6232-3
- Mertens, P. P. C., Maan, S., Samuel, A., Attoui, H., Fauquet, C. M., Mayo, M. A. et al. (2005). Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. Fauquet, 447-454.
- Muhire, B.M., Varsani, A. ve Martin, D.P. (2014). SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One, 9, 0108277. https://doi.org/10.1371/journal.pone.0108277
- Pappu, H.R., Hellier, B.C. ve Dugan, F.M. (2005). First report of Onion yellow dwarf virus, Leek yellow stripe virus, and Garlic common latent virus in garlic in Washington State. Plant Disease, 89(2), 205-205. https://doi.org/10.1094/PD-89-0205C
- Takaki, F., Sano, T., Yamashita, K., Fujita, T., Ueda, K., ve Kato, T. (2005). Complete nucleotide sequences of attenuated and severe isolates of Leek yellow stripe virus from garlic in northern Japan: Identification of three distinct virus types in garlic and leek world-wide. Archives of Virology, 150(6), 1135-1149. https://doi.org/10.1007/s00705-004-0482-9
- Tuzlalı, H.T. (2018). Güney Marmara Bölgesi’nde Allıum Cinsi Bitkilerde Potyvirüslerin Tanılanması ve Karakterizasyonu (Doktora Tezi). Erişim adresi: https://tez.yok.gov.tr/UlusalTezMerkezi
- Wylie, S. J., Adams, M., Chalam, C., Kreuze, J., López-Moya, J. J., Ohshima, K. et al. (2017). ICTV virus taxonomy profile: Potyviridae. Journal of General Virology, 98(3), 352. https://doi.org/10.1099/jgv.0.000740
- Zheng, L., Rodoni, B. C., Gibbs, M. J. ve Gibbs, A. J. (2010). A novel pair of universal primers for the detection of potyviruses. Plant Pathology, 59(2), 211-220. https://doi.org/10.1111/j.1365-3059.2009.02201.x
There are 19 citations in total.
Details
| Primary Language | Turkish |
|---|---|
| Subjects | Agricultural Engineering (Other) |
| Journal Section | Araştırma Makalesi |
| Authors | |
| Project Number | 2209-A |
| Publication Date | May 22, 2020 |
| Acceptance Date | May 8, 2020 |
| Published in Issue | Year 2020 Volume: 6 Issue: 1 |
