The molecular characterization of the coat protein sequence and differentiation of CMV- subgroup I on tobacco from native flora in Turkey

Authors

  • Mustafa USTA Van Yuzuncu Yil University, Faculty of Agriculture, Department of Plant Protection, Van (TR)
  • Abdullah GÜLLER Bingöl University, Faculty of Agriculture, Department of Plant Protection, Bingöl (TR)
  • Abidin GÜNAY Van Yuzuncu Yil University, Faculty of Agriculture, Department of Plant Protection, Van (TR)

DOI:

https://doi.org/10.15835/nbha48211822

Keywords:

characterization; cloning; cucumber mosaic virus; phylogeny; subgroup

Abstract

Cucumber mosaic virus (CMV) has a broad plant-host range and a wide ecological zone distribution. Virus-like symptoms were observed on tobacco fields of Adiyaman province (Turkey) showing conspicuous mottling, greenish mosaic patterns and severe malformations of leaves. A total of forty tobacco samples tested positive against CMV by reverse transcription polymerase chain reaction (RT-PCR) using coat protein gene specific primers. Five randomly chosen CMV isolates were cloned into pGEM T-Easy vector and transformed into Escherichia coli JM109 strain. The recombinant bacterial clones containing insert-DNA were further purified and sequenced bidirectionally. In multiplex-RT-PCR studies carried out, it was found that all 40 CMV isolates belong to Subgroup I by resulting a 593 bp long DNA fragments. CMV subgroup IA was found to predominate in 4 out of 5 tobacco samples and CMV subgroup IB was found in 1 out of 5 CMV-positive samples by comparing the isolates with CMV reference isolates in phylogenetic tree. However, no Subgroup II sequences were found by multiplex RT-PCR using discriminating primers. The nucleic acid sequences were analyzed for the investigation of diversity of coat protein (CP) sequences of 5 CMV isolates. The sequence similarity ranged from 94.2-100% with the CMV subgroup I isolates infecting diverse plants in other regions of the world. The evolutionary tree revealed that the CMV IA Adiyaman isolates exhibited a genetic affinity with Australian and Spanish isolates. However, the CMV IB Adiyaman isolate showed a close genetic relationship with only the Australian isolates. To our knowledge, this study shows for the first time the occurrence of CMV IA and IB isolates infecting cultured tobacco plants in Adiyaman province.

References

Akinyemi IA, Wang F, Zhou B, Qi S, Wu Q (2016). Eco-genomic survey of plant viruses infecting tobacco by next generation sequencing. Virology Journal 13:181. https://doi.org/10.1186/s12985-016-0639-7

Arafati N, Farzadfar S, Pourrahim R (2013). Characterization of coat protein gene of cucumber mosaic virus isolates in Iran. Iranian Journal of Biotechnology 1(2):109-114. https://doi.org/10.5812/ijb.10715

Ayo-John EI, Hughes Jd’A (2014). Identification of cucumber mosaic virus (CMV) isolates infecting Musa spp. and vegetable crops in Southern Nigeria. International Journal of Virology 10:204-210. https://doi.org/10.3923/ijv.2014.204.210

Ayo-John EI, Hughes DJA, Ekpo EJA (2008). Survey for CMV in field samples of Musa spp. in southern Nigeria. International Journal of Pest Management 54:167-172. https://doi.org/10.1080/09670870701875235

Beler Ö, Acıkgöz S (2005). Detection of some virus diseases in olive trees and trees in Aegean and Marmara regions by ELISA test. ADU Journal of Faculty of Agriculture 2(1):79-84.

Chatzivassiliou EK (2008). Management of the spread of tomato spotted wilt virus in tobacco crops with insecticides based on estimates of trips infestation and virus incidence. Plant Disease 92:1012-1020. https://doi.org/10.1094/PDIS-92-7-1012

Chen S, Gu H, Wang X, Chen J, Zhu W (2011). Multiplex RT-PCR detection of Cucumber mosaic virus subgroups and Tobamoviruses infecting tomato using 18S rRNA as an internal control. Acta Biochimica et Biophysica Sinica 43:465-471. https://doi.org/10.1093/abbs/gmr031

Chen W, Dai J, Zhang H, Jiao H, Cheng J, Wu Y (2014). Concentration and detection of tobacco etch virus from irrigation water using real-time PCR. Turkish Journal of Agriculture and Forestry 38:471-477. https://doi.org/10.3906/tar-1305-98

Chikh Ali M, Omar AMS, Maoka T, Natsuaki KT, Natsuaki T (2012). Characterization of potato and tobacco isolates of cucumber mosaic virus from Syria and the first report on CMV satellite RNA from potato. Phytopathologia Mediterranea 51(1):3-10.

Caglar BK (2006). Characterization of isolates of cucumber mosaic virus in melon, tomato and pepper by biological, serological and molecular methods and their effect on the virus of satellite RNAs. PhD Thesis, Cukurova University, Adana, Turkey.

Culal Kılıc H, Yardımcı N (2012). Cucumber mosaic virus in çine plain bean fields in Burdur province. Mehmet Akif Ersoy University, Journal of the Institute of Science and Technology 3(2):12-15.

Culal Kılıc H, Yardımcı N, Toplu S, Konu A (2015). Cucumber mosaic virus and pepper mild mottle virus in pepper growing areas in Burdur province, Turkey. International Journal of Scientific and Technological Research 1:1.

Dai J, Cheng J, Huang T, Zheng X, Wu Y (2012). A multiplex reverse transcription PCR assay for simultaneous detection of five tobacco viruses in tobacco plants. Journal of Virological Methods 183:57–62.

https://doi.org/10.1016/j.jviromet.2012.03.029

De Bokx JA, Huttinga H (1981). Potato virus Y. CMI/AAB Descriptions of Plant Viruses 242:6.

Doolittle SP (1916). A new infectious mosaic disease of cucumber. Phytopathology 6:145-147.

Eni AO, Lava Kumar P, Asiedu R, Alabi OJ, Naidu RA, Rey MEC (2013). Characterization of cucumber mosaic virus isolated from yam (Dioscorea spp.) in West Africa. African Journal of Biotechnology 12(22):3472-3480. https://doi.org/10.1094/pdis-92-5-0833b

EPPO/CABI (1996b). Tomato ringspot nepovirus. In: Quarantine pests for Europe. 2nd edition (Ed. by Smith IM, McNamara DG, Scott PR, Holderness M). Cab International, Wallingford, UK.

Ergün M, Semih E, Paylan IC (2013). Cucumber mosaic virus in globe artichoke in Turkey. Canadian Journal of Plant Pathology 35(4):514-517. https://doi.org/10.1080/07060661.2013.833987

Erkan S, Gümüs M, Paylan IC, Duman I, Ergün M (2013). Determination of viral factors in some winter vegetables in İzmir province and its surroundings. Ege University Journal of Faculty of Agriculture 50(3):311-322.

Eyvazi A, Dizadji A, Rastgou M, Koohi Habibi M (2015). Bioassay and phylogeny of five Iranian isolates of cucumber mosaic virus from different hosts based on CP gene sequence. Plant Protection Science 51(4):200-207. https://doi.org/10.17221/80/2014-pps

FAO (2013). United Nations Food and Agriculture Organization Agricultural Statistics. Retrieved 2013 March 24 from http://faostat.fao.org/

Farzadfar S, Pourrahim R, Arafati N (2013). Molecular identification of cucumber mosaic virus subgroup IB isolates in South Iran. Journal of Plant Pathology 95(2):423-428.

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

Garcia-Arenal F, Palukaitis P (2008). Cucumber mosaic virus. In: BWJ Mahy and MHV van Regenmortel (Eds.). Desk encyclopedia of plant and fungal virology. Elsevier Amsterdam pp 171-176.

Gökdag S, Karanfil A, Korkmaz S (2016). Determination of turnip mosaic virus and cucumber mosaic virus in Canakkale spinach fields. In: Garden special issue (VII). National Horticultural Congress Proceedings (2): Vegetable-Viticulture-Ornamental Plants pp 166-170.

Gümüs M, Erkan S, Tok S (2004). Research on the detection of viral factors in the seeds of some cucurbit species. Journal of Ege University Faculty of Agriculture 41(1):49-56.

Güngör M, Uzunbacak H, Kutluk-Yilmaz ND, Sevik MA (2017). Identification of viruses that cause infection in spinach production areas of Samsun province. Anadolu Journal of Agricultural Sciences 32:164-168.

Günay A (2019). Investigation of some tobacco viruses by multiplex RT-PCR method in Adıyaman province tobacco production fields and molecular characterization of some virus isolates. MSc Dissertation, Van Yuzuncu Yil University.

Haase A, Richter J, Rabenstein F (1989). Monoclonal antibodies for detection and serotyping of cucumber mosaic virus. Phytopathology 127:129-136. https://doi.org/10.1111/j.1439-0434.1989.tb01121.x

Hord MJ, Garcìa A, Villalobos H, Rivera C, Macaya G (2001). Field survey of Cucumber mosaic virus subgroups I and II in crop plants in Costa Rica. Plant Disease 85:952-954. https://doi.org/10.1094/PDIS.2001.85.9.952

Jalender P, Bhat BN, Anitha K., Vijayalakshmi K (2017). Studies on transmission of cucumber mosaic virus (CMV) by sap inoculation in tomato. International Journal of Pure and Applied Bioscience 5(4):1908-1912. https://doi.org/10.18782/2320-7051.5764

Jaspars EMJ, Bos L (1980). Alfalfa mosaic virus. CMI/AAB Descriptions of Plant Viruses 229:7.

Kaplan IB, Gal-On A, Palukaitis P (1997). Characterization of cucumber mosaic virus. III. Localization of sequences in the movement protein controlling systemic infection in cucurbits. Virology 230:343-349. https://doi.org/10.1006/viro.1997.8468

Karanfil A, Korkmaz S (2017). Detection of cucumber mosaic virus (Cucumber mosaic virus; CMV) in the cowpea production areas of Çanakkale province and its molecular characterization. Plant Protection Bulletin 57(3):293-304. https://doi.org/10.16955/bitkorb.340046

Karanfil A, Soylu B, Korkmaz S (2016). Investigation of cucumber mosaic virus infection in bulbous ornamental plants by serological and molecular methods in Çanakkale province and its districts. Trakya University Journal of Natural Sciences 17(2):105-110.

Koc G, Fidan H (2017). In Turkey, cucumber mosaic virus (CMV) for a host of evergreens: Polygala myrtifolia. Derim 34(1):29-36. https://doi.org/10.16882/derim.2017.305281

Kumar S, Stecher G, Tamura, K (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870-1874. https://doi.org/10.1093/molbev/msw054

Kumari R, Bhardwaj P, Singh L, Zaidi AA, Hallan V (2013). Biological and molecular characterization of cucumber mosaic virus subgroup II isolate causing severe mosaic in cucumber. Indian Journal of Virology 24(1):27-34. https://doi.org/10.1007/s13337-012-0125-9

Kurtoglu A, Korkmaz S (2018). Determination and molecular characterization of cucumber mosaic virus (CMV) infection on spinach production fields of Çanakkale province, Turkey. The Journal of Turkish Phytopathology 47(2):43-51.

Lin HX, Rubio L, Smythe A, Jiminez M, Falk BW (2003). Genetic diversity and biological variation among California isolates of cucumber mosaic virus. Journal of General Virology 84:249-258. https://doi.org/10.1099/vir.0.18673-0

Moury B (2004). Differential selection of genes of cucumber mosaic virus subgroups. Molecular Biology and Evolution 21:1602-1611. https://doi.org/10.1093/molbev/msh164

Nagendran K, Priyanka R, Aravintharaj R, Balaji CG, Swamy Prashant, Bagewadi Basavaraj, … Karthikeyan G (2018). Characterization of cucumber mosaic virus infecting snake gourd and bottle gourd in India. Physiological and Molecular Plant Pathology 103:102-106. https://doi.org/10.1016/j.pmpp.2018.05.010

Nakazono-Nagaoka E, Suzuki M, Kosaka Y, Natsuaki T (2005). RT-PCR-RFLP analysis for evaluating cross protection by an attenuated isolate of cucumber mosaic virus. Journal of General Plant Pathology 71(3):243-246. https://doi.org/10.1007/s10327-005-0192-5

Özdag Y, Sertkaya G (2017). Investigation on viruses causing yellowing disease in pepper in Hatay-Turkey. Journal of Agricultural Faculty of Mustafa Kemal University 22(1):16-22.

Palukaitis P, Garcia-Arenal F (2003). Cucumber mosaic virus. AAB Descriptions of Plant Viruses 400.

Palukaitis P, Roossinck MJ, Dietzgen RG, Francki RI (1992). Cucumber mosaic virus. Advances in Virus Research 41:281-348. https://doi.org/10.1016/s0065-3527(08)60039-1

Park TS, You JW, Park JS, Jeong RD, Hong JS (2018). First report of cucumber mosaic virus infecting Solanum pseudocapsicum in Korea. Journal of Plant Pathology 100:147. https://doi.org/10.1007/s42161-018-0037-7

Rizos H, Gunn LV, Pares RD, Gillings RM (1992). Differentiation of cucumber mosaic virus isolates using the polymerase chain reaction. Journal of General Virology 73:2099-2103. https://doi.org/10.1099/0022-1317-73-8-2099

Rodríguez Pardina P, Ojeda M, Biderbost E, Di Feo L (2013). Detection and characterization of a cucumber mosaic virus isolate infecting peperina, a species native to Argentina. Agriscientia 30(2):79-85. https://doi.org/10.31047/1668.298x.v30.n2.8993

Roossinck MJ (2002). Evolutionary history of cucumber mosaic virus deduced by phylogenetic analyses. Journal of Virology. 76:3382–3387. https://doi.org/10.1128/jvi.76.7.3382-3387.2002

Sarı S (2015). Characterization of cucumber mosaic virus (CMV) isolates causing infection in summer vegetables grown in Samsun province and investigation of host-simptom-satellite RNA relationships. MSc Dissertation, Ondokuz Mayıs University.

Sclavounos AP, Voloudakis AE, Arabatzis C, Kyriakopoulou PE (2006). A severe Hellenic CMV tomato isolate: symptom variability in tobacco, characterization and discrimination of variants. European Journal of Plant Pathology 115:163-172. https://doi.org/10.1007/s10658-006-0010-8

Sertkaya G (2015). Investigation of some viruses in the areas of lettuce and spinach in Hatay province. Mustafa Kemal University Journal of the Faculty of Agriculture 20(1):7-12.

Sevik MA (2012). Natural occurrence of cucumber mosaic virus infecting water mint (Mentha aquatica) in Antalya and Konya, Turkey. The Journal Acta Botanica Croatica 71(1):187-193. https://doi.org/10.2478/v10184-011-0052-7

Sevik MA (2017). Natural occurrence of cucumber mosaic virus infecting broccoli in Turkey. Virus Disease 28(2):218-219. https://doi.org/10.1007/s13337-017-0373-9

Sevik MA, Akcura C (2011). Occurrence of cucumber mosaic virus infecting parsley (Petroselinum crispum) in Turkey. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39(1):30-33. https://doi.org/10.15835/nbha3915598

Shevchenko TP, Tymchyshyn OV, AlDalain E, Bysov AS, Budzanivska IG, Shevchenko OV, Polishchuk VP (2015). The first evidence of subgroup IB isolates of cucumber mosaic virus in Ukraine. Biopolymers and Cell 31(1):57-62. https://doi.org/10.7124/bc.0008cd

Singh Z, Jones RAC, Jones MGK (1995). Identification of cucumber mosaic virus subgroup I isolates from banana plants affected by infectious chlorosis disease using RT-PCR. Plant Disease 79:713-716. https://doi.org/10.1094/pd-79-0713

Tian Z, Qiu J, Yu J, Han C, Liu W (2009). Competition between cucumber mosaic virus subgroup I and II isolates in tobacco. Journal of Phytopathology 157:457-464. https://doi.org/10.1111/j.1439-0434.2008.01531.x

Tsitsipis JA, Gargalianou I, Eythimiou K, Chatzivassiliou EK, Katis NI (2001). Aphid population fluctuation and spread of potato virus Y (PVY) and cucumber mosaic virus (CMV) in tobacco crops in Greece and Italy. Abstracts, 6th International Symposium on Aphids. Aphids in a New Millennium. Rennes, France pp 169.

TUIK (2015). Turkey Statistical Institute (TUIK). Retrieved 2017 February 10 from https://biruni.tuik.gov.tr/bitkiselapp/bitkisel.zul

Uzunogulları N, Gümüs M (2015). Detection of cucumber mosaic virus (CMV) causing natural infection in some cultivated plants in the Marmara Region. Trakya University Journal of Natural Sciences 16(1):9-15.

Valand GB, Muniyappa V (1992). Epidemiology of tobacco leaf curl virus in India. Annals of Applied Biology 120(2):257-267. https://doi.org/10.1111/j.1744-7348.1992.tb03423.x

Yardımcı N, Culal Kılıc H, Kör A (2015). Identification of cucumber mosaic virus (CMV) on Squash (Cucurbita pepo L.) cultivars in Lakes region of Turkey. Fresenius Environmental Bulletin 24:2.

Yu C, Wu J, Zhou X (2005). Detection and subgrouping of cucumber mosaic virus isolates by TAS-ELISA and immunocapture RT-PCR. Journal of Virological Methods 123:155-161. https://doi.org/10.1016/j.jviromet.2004.09.014

Zhang J, Wang R, Song J, Luo Z, Yang J, Lin F (2013). One-step multiplex RT-PCR for simultaneous detection of four viruses in tobacco. Journal of Phytopathology 161:92-97. https://doi.org/10.1111/jph.12032

Zhang L, Hanada K, Palukaitis P (1994). Mapping local and systemic symptom determinants of cucumber mosaic cucumovirus in tobacco. Journal of General Virology 75:3185-3191. https://doi.org/10.1099/0022-1317-75-11-3185

Zhu F, Che YP, Zhou YK, Cheng SC, Liu Z, Ji ZL (2018). First report of cucumber mosaic virus infecting Arachis hypogaea in Jiangxi Province in China. Journal of Plant Pathology 100:337. https://doi.org/10.1007/s42161-018-0056-4

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Published

2020-06-30

How to Cite

USTA, M., GÜLLER, A. ., & GÜNAY, A. . (2020). The molecular characterization of the coat protein sequence and differentiation of CMV- subgroup I on tobacco from native flora in Turkey. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 48(2), 523–534. https://doi.org/10.15835/nbha48211822

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Vol. 48 No. 2 (2020)

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Research Articles
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DOI: 10.15835/nbha48211822

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Copyright (c) 2020 Mustafa USTA, Abdullah GÜLLER, Abidin GÜNAY

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