Articles
Characterization of two Cucumber mosaic virus isolates infecting Allium cepa in Turkey
Adyatma I. SANTOSA- Filiz ERTUNC
Published 2021-05-13
Keywords
- Cucumber mosaic virus (CMV),
- onion,
- phylogenetic analysis,
- host indexing
How to Cite
[1]
A. I. SANTOSA and F. ERTUNC, “Characterization of two Cucumber mosaic virus isolates infecting Allium cepa in Turkey”, Phytopathol. Mediterr., vol. 60, no. 1, pp. 13–21, May 2021.
Funding data
-
Ankara Universitesi
Grant numbers Project No. 18H0447001, titled “Detection of Viral Infection Sources on Onion Production Areas”
Abstract
Cucumber mosaic virus (CMV) is polyphagous, infecting plants in several families. CMV has occurred as a minor pathogen in Allium crops in several Mediterranean countries, but little was known of the virus naturally infecting Allium spp. This study completed molecular and biological characterization of CMV-14.3Po and CMV-15.5Po, two newly identified CMV isolates infecting onion (Allium cepa L.) in Turkey. Phylogenetic, and nucleotide and amino acid sequence identity analyses of partial RNA2 and RNA3 of the two isolates showed that they were very similar to other CMV isolates from Mediterranean, European, and East Asian countries. Phylogenetic analysis of the partial sequence of RNA3 also showed that the onion isolates belong to subgroup IA. Onion isolates were mechanically transmissible, and caused mild leaf malformation on onion, severe leaf malformation and stunting on garlic (Allium sativus L.), and mosaic and mottle on cucumber (Cucumis sativus L.) and melon (Cucumis melo L.).
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References
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Brunt A.A., Crabtree K., Dallwitz M.J., Gibbs A.J., Watson L., 1996. Plant Viruses Online: Description and Lists from the VIDE Database. Cucumber mosaic cucumovirus. Available at: http://bio-mirror.im.ac.cn/mirrors/pvo/vide/descr267.htm. Accessed January 31, 2020.
Chen J., Wei C.B., Zheng H.Y., Shi Y.H., Adams M.J., ... Chen J.P., 2005. Characterisation of the welsh onion isolate of Shallot yellow stripe virus from China. Archives of Virology 150: 2091–2099. https://doi.org/10.1007/s00705-005-0580-3
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Divéki Z., Salánki K., Balázs E., 2004. The necrotic pathotype of the Cucumber mosaic virus (CMV) Ns strain is solely determined by amino acid 461 of the 1a protein. Molecular Plant-Microbe Interactions 17(8): 837–845. https://doi.org/10.1094/mpmi.2004.17.8.837
Dovas C.I., Volvas C., 2003. Viruses infecting Allium spp. in Southern Italy. Journal of Plant Pathology 85(2): 135. http://dx.doi.org/10.4454/jpp.v85i2.1022
Fajardo T.V.M., Nishijima M., Buso J.A., Torres A.C., Ávila A.C., Resende R.O., 2001. Garlic viral complex: identification of potyviruses and carlavirus in central Brazil. Fitopatologia Brasileira 26: 619–626. https://doi.org/10.1590/S0100-41582001000300007
Fidan H., 2010. Sarımsak, soğan ve pırasadaki virüs hastalıklarını saptanması ve Taşköprü 56 sarımsak tipinin en yaygın virüse karşı reaksiyonunun belirlenmesi. PhD Thesis, Cukurova University, Adana, Turkey, 163 pp (in Turkish).
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Gera A., Lesemann D.E., Cohen J., Franck A., Levy S., Salomo R., 1997. The natural occurrence of Turnip Mosaic Potyvirus in Allium ampeloprasum. Journal of Phytopathology 145(7): 289–293. https://doi.org/10.1111/j.1439-0434.1997.tb00403.x
Hall B.G., 2013. Building phylogenetic trees from molecular data with MEGA. Molecular Biology and Evolution 30(5): 1229–1235. https://doi.org/10.1093/molbev/mst012
Hayes R.J., Buck K.W., 1990. Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA Polymerase. Cell 63(2): 363–368. https://doi.org/10.1016/0092-8674(90)90169-f
Hill S.A., 1984. Methods in Plant Virology. Blackwell Scientific Publications, Oxford, United Kingdom, 167 pp.
Majumder S., Baranwal V.K,. Joshi S., 2008. Simultaneous detection of Onion yellow dwarf virus and Shallot latent virus in infected leaves and cloves of garlic by Duplex RT-PCR. Journal of Plant Pathology 90(2): 371–374. https://doi.org/10.1007/s13337-010-0008-x
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(9): e108277. https://doi.org/10.1371/journal.pone.0108277
Nam M., Lee Y., Park C.H., Lee M., Bae Y., ... Lee S., 2015. Development of multiplex RT-PCR for simultaneous detection of garlic viruses and the incidence of garlic viral disease in garlic genetic resources. The Plant Pathology Journal 31(1): 90–96. https://doi.org/10.5423/PPJ.NT.10.2014.0114
Ohshima K., Matsumoto K., Yasaka R., Nishiyama M., Soejima K., ... Takeshita M., 2016. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology 487: 188–197. https://doi.org/10.1016/j.virol.2015.09.024
Palukaitis P., Garcia-Arenal F., 2003. Cucumoviruses. Advances in Virus Research 62: 241–323. https://doi.org/10.1016/s0065-3527(03)62005-1
Parrano L., Afunian M., Pagliaccia D., Douhan G., Vidalakis G., 2012. Characterization of viruses associated with garlic plants propagated from different reproductive tissues from Italy and other geographic regions. Phytopathologia Mediterranea 51(3): 549–565. https://doi.org/10.14601/Phytopathol_Mediterr-10479
Presting G.G., Smith O.P., Brown C.R., 1995. Resistance to Potato leafroll virus in Potato plants transformed with the Coat protein gene or with vector control constructs. Phytopathology 85: 436–442. https://doi.org/10.1094/Phyto-85-436
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. Journal of Virology 73(8): 6752–6758. http://www.ncbi.nlm.nih.gov/pmc/articles/pmc112760/
Santosa A.I., Ertunc F., 2020. Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara province, Turkey. Journal of Plant Diseases and Protection. https://doi.org/10.1007/s41348-020-00347-5
Sevik M.A., Akcura C., 2013. Viruses occurring in onion crop in Amasya province, the major onion producing region in Turkey. Indian Journal of Virology 24(1): 78–81. https://doi.org/10.1007/s13337-012-0114-z
Shahraeen N., Lesemann D.E., Ghotbi T., 2008. Survey for viruses infecting onion, garlic and leek crops in Iran. Bulletin OEPP/EPPO Bulletin 38: 131–135. https://doi.org/10.1111/j.1365-2338.2008.01198.x
Stefanac Z., 1980. Cucumber mosaic virus in Garlic. Acta Botanica Croatica 39: 21–26.
Stefanac Z., Milicic D., 1992. Observations on infection of garlic (Allium sativum L.) with Cucumber mosaic virus. Acta Botanica Croatica 51: 1–5.
Sujitha A., Bhaskara Reddy B.V., Sivaprasad Y., Usha R., Sai Gopal D.V.R., 2012. First report of Groundnut bud necrosis virus infecting onion (Allium cepa). Australasian Plant Disease Notes 7: 183–187. https://doi.org/10.1007/s13314-012-0080-8
Tamura K., 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. https://doi.org/10.1093/oxfordjournals.molbev.a040752
Tomassoli L., Tiberini A., Masenga V., Vicchi V., Turina M., 2009. Characterızatıon of Iris yellow spot virus isolates from onion crops in Northern Italy. Journal of Plant Pathology 91(3): 733–739.
Ward L.I., Perez-Egusquiza Z., Fletcher J.D., Clover G.R.G., 2009. A survey of viral diseases of Allium crops in New Zealand. Australasian Plant Pathology 38: 533–539. https://doi.org/10.1071/AP09039
Alfaro-Fernandez A., Villaescusa F.J., Hermoso de Mendoza A., Ferrandiz J.C., Sanjuan S., Font San Ambrosio M.I., Unpublished. First report of aster yellows and stolbur phytoplasma infecting commercial leek (Allium porrum L.) in Spain.
Bag S., Schwartz H.F., Cramer C.S., Havey M.J., Pappu H.R., 2015. Iris yellow spot virus (Tospovirus: Bunyaviridae): From obscurity to research priority. Molecular Plant Pathology 16(3): 224–237. https://doi.org/10.1111/mpp.12177
Boccard F., Baulcombe D., 1993. Mutational analysis of cis acting sequences and gene function in RNA3 of Cucumber mosaic virus. Virology 193: 563–578. https://doi.org/10.1006/viro.1993.1165
Brunt A.A., Crabtree K., Dallwitz M.J., Gibbs A.J., Watson L., 1996. Plant Viruses Online: Description and Lists from the VIDE Database. Cucumber mosaic cucumovirus. Available at: http://bio-mirror.im.ac.cn/mirrors/pvo/vide/descr267.htm. Accessed January 31, 2020.
Chen J., Wei C.B., Zheng H.Y., Shi Y.H., Adams M.J., ... Chen J.P., 2005. Characterisation of the welsh onion isolate of Shallot yellow stripe virus from China. Archives of Virology 150: 2091–2099. https://doi.org/10.1007/s00705-005-0580-3
De Blas C., Borja M.J., Saiz M., Romero J., 1994. Broad spectrum detection of Cucumber mosaic virus (CMV) using the Polymerase Chain Reaction. Journal of Phytopathology 141(3): 323–329. https://doi.org/10.1111/j.1439-0434.1994.tb01476.x
Divéki Z., Salánki K., Balázs E., 2004. The necrotic pathotype of the Cucumber mosaic virus (CMV) Ns strain is solely determined by amino acid 461 of the 1a protein. Molecular Plant-Microbe Interactions 17(8): 837–845. https://doi.org/10.1094/mpmi.2004.17.8.837
Dovas C.I., Volvas C., 2003. Viruses infecting Allium spp. in Southern Italy. Journal of Plant Pathology 85(2): 135. http://dx.doi.org/10.4454/jpp.v85i2.1022
Fajardo T.V.M., Nishijima M., Buso J.A., Torres A.C., Ávila A.C., Resende R.O., 2001. Garlic viral complex: identification of potyviruses and carlavirus in central Brazil. Fitopatologia Brasileira 26: 619–626. https://doi.org/10.1590/S0100-41582001000300007
Fidan H., 2010. Sarımsak, soğan ve pırasadaki virüs hastalıklarını saptanması ve Taşköprü 56 sarımsak tipinin en yaygın virüse karşı reaksiyonunun belirlenmesi. PhD Thesis, Cukurova University, Adana, Turkey, 163 pp (in Turkish).
Finetti Sialer M.M., Cillo F., Barbarossa L., Gallitelli D., 1999. Differentiation of Cucumber mosaic virus subgroups by RT-PCR RFLP. Journal of Plant Pathology 81(2): 145–148. http://dx.doi.org/10.4454/jpp.v81i2.1059
Gera A., Lesemann D.E., Cohen J., Franck A., Levy S., Salomo R., 1997. The natural occurrence of Turnip Mosaic Potyvirus in Allium ampeloprasum. Journal of Phytopathology 145(7): 289–293. https://doi.org/10.1111/j.1439-0434.1997.tb00403.x
Hall B.G., 2013. Building phylogenetic trees from molecular data with MEGA. Molecular Biology and Evolution 30(5): 1229–1235. https://doi.org/10.1093/molbev/mst012
Hayes R.J., Buck K.W., 1990. Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA Polymerase. Cell 63(2): 363–368. https://doi.org/10.1016/0092-8674(90)90169-f
Hill S.A., 1984. Methods in Plant Virology. Blackwell Scientific Publications, Oxford, United Kingdom, 167 pp.
Majumder S., Baranwal V.K,. Joshi S., 2008. Simultaneous detection of Onion yellow dwarf virus and Shallot latent virus in infected leaves and cloves of garlic by Duplex RT-PCR. Journal of Plant Pathology 90(2): 371–374. https://doi.org/10.1007/s13337-010-0008-x
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(9): e108277. https://doi.org/10.1371/journal.pone.0108277
Nam M., Lee Y., Park C.H., Lee M., Bae Y., ... Lee S., 2015. Development of multiplex RT-PCR for simultaneous detection of garlic viruses and the incidence of garlic viral disease in garlic genetic resources. The Plant Pathology Journal 31(1): 90–96. https://doi.org/10.5423/PPJ.NT.10.2014.0114
Ohshima K., Matsumoto K., Yasaka R., Nishiyama M., Soejima K., ... Takeshita M., 2016. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology 487: 188–197. https://doi.org/10.1016/j.virol.2015.09.024
Palukaitis P., Garcia-Arenal F., 2003. Cucumoviruses. Advances in Virus Research 62: 241–323. https://doi.org/10.1016/s0065-3527(03)62005-1
Parrano L., Afunian M., Pagliaccia D., Douhan G., Vidalakis G., 2012. Characterization of viruses associated with garlic plants propagated from different reproductive tissues from Italy and other geographic regions. Phytopathologia Mediterranea 51(3): 549–565. https://doi.org/10.14601/Phytopathol_Mediterr-10479
Presting G.G., Smith O.P., Brown C.R., 1995. Resistance to Potato leafroll virus in Potato plants transformed with the Coat protein gene or with vector control constructs. Phytopathology 85: 436–442. https://doi.org/10.1094/Phyto-85-436
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. Journal of Virology 73(8): 6752–6758. http://www.ncbi.nlm.nih.gov/pmc/articles/pmc112760/
Santosa A.I., Ertunc F., 2020. Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara province, Turkey. Journal of Plant Diseases and Protection. https://doi.org/10.1007/s41348-020-00347-5
Sevik M.A., Akcura C., 2013. Viruses occurring in onion crop in Amasya province, the major onion producing region in Turkey. Indian Journal of Virology 24(1): 78–81. https://doi.org/10.1007/s13337-012-0114-z
Shahraeen N., Lesemann D.E., Ghotbi T., 2008. Survey for viruses infecting onion, garlic and leek crops in Iran. Bulletin OEPP/EPPO Bulletin 38: 131–135. https://doi.org/10.1111/j.1365-2338.2008.01198.x
Stefanac Z., 1980. Cucumber mosaic virus in Garlic. Acta Botanica Croatica 39: 21–26.
Stefanac Z., Milicic D., 1992. Observations on infection of garlic (Allium sativum L.) with Cucumber mosaic virus. Acta Botanica Croatica 51: 1–5.
Sujitha A., Bhaskara Reddy B.V., Sivaprasad Y., Usha R., Sai Gopal D.V.R., 2012. First report of Groundnut bud necrosis virus infecting onion (Allium cepa). Australasian Plant Disease Notes 7: 183–187. https://doi.org/10.1007/s13314-012-0080-8
Tamura K., 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. https://doi.org/10.1093/oxfordjournals.molbev.a040752
Tomassoli L., Tiberini A., Masenga V., Vicchi V., Turina M., 2009. Characterızatıon of Iris yellow spot virus isolates from onion crops in Northern Italy. Journal of Plant Pathology 91(3): 733–739.
Ward L.I., Perez-Egusquiza Z., Fletcher J.D., Clover G.R.G., 2009. A survey of viral diseases of Allium crops in New Zealand. Australasian Plant Pathology 38: 533–539. https://doi.org/10.1071/AP09039