Chickpea chlorotic dwarf virus: genome sequence of the virus from two new natural hosts, associated alphasatellite and demonstration of the pathogenesis in okra plant

Document Type : Research Article

Authors

1 Department of Plant Protection, College of Agriculture, University of Jiroft, Jiroft, Iran

2 Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran

Abstract

Chickpea chlorotic dwarf virus (Mastrevirus, Geminiviridae) is a destructive geminivirus worldwide. In this study, symptomatic okra and wild jute samples showing typical geminivirus symptoms were collected from Jiroft farms and circular molecules of extracted DNA were enriched using rolling circle amplification (RCA) method followed by cloning and sequencing of RCA products of two selective samples from okra and wild jute. Sequence analysis showed that two isolates belong to strain CpCDV-F. Attempts to recover associated alpha- and betasatellite molecules from two plant samples using polymerase chain reaction assay resulted in detection of Gossypium darwinii symptomless alphasatellite (GDarSLA) only in wild jute sample. Sequence analyses indicated that two new CpCDV isolates shared nucleotide identity of 98% with each other and two viral and one alphasatellite sequences are closely related to Iranian Genbank isolates. Pathogenesis tests using previously constructed infectious clone of CpCDV led to appearance of yellowing and dwarfing in agroinoculated okra seedlings. Based on the results of this study, okra and wild jute plants are reported as new hosts of the CpCDV in Iran and wild jute is the new virus host in the world.

Keywords

References

Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3): 403-10.
Askari F., Heydarnejad J., Vaziri S., Esmaeili M. and Massumi H. 2021. Chickpea chlorotic dwarf virus: natural hosts and genome characterization of a virus isolate in eastern and southern Iran. Iranian Journal of Plant Pathology 57(3): 203-216.
Askari F., Heydarnejad J., Vaziri S., Sadeghi-Majd J., Kamali M. and Massumi H. 2018. Chickpea chlorotic dwarf virus a polyphagous mastrevirus infecting crops and vegetables in Iran. The Proceeding of the 23rd Iranian Plant Protection Congress, Iran, Gorgan. pp 612-13.
Briddon R.W., Bull S.E., Mansoor S., Amin I. and Markham P. G. 2002. Universal primers for the PCR-mediated amplification of DNA β; a molecule associated with some monopartite begomoviruses. Molecular Biotechnology 20: 315–318.
Brown J.K., Fauquet C.M., Briddon R.W., Zerbini M., Moriones E. and Navas-Castillo J. 2012. Geminiviridae. pp 351–373. In: King A.M.Q., Adams M.J., Carstens E.B. and Lefkowitz E.J. (Eds.), Virus taxonomy: classification and nomenclature of viruses: ninth report of the International Committee on Taxonomy of Viruses. Elsevier/Academic Press, San Diego, USA.
Claverie S., Bernardo P., Kraberger S., Hartnady P., Lefeuvre P., Lett J.M., Galzi S., Filloux D., Harkins G.W., Varsani A., Martin D.P. and Roumagnac P. 2018. From spatial metagenomics to molecular characterization of plant viruses: a geminivirus case study. pp 55–83. In: Malmstrom C.M. (Ed.), Advances in Virus Research. Environmental Virology and Virus Ecology. Academic Press, New York, USA.
Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-7.
Farzadfar Sh., Pourrahim R., Golnaraghi A.R. and Ahoonmanesh A. 2008. PCR detection and partial molecular characterization of Chickpea chlorotic dwarf virus in naturally infected sugar beet plants in Iran. Journal of Plant Pathology 90: 247-251.
Fiallo-Olivé E., Lett J.M., Martin D.P., Roumagnac P., Varsani A., Zerbini F.M. and Navas-Castillo J. 2021. ICTV virus taxonomy profile: Geminiviridae. Journal of General Virology 102(12): 001696.
Gnanasekaran P., Chakraborty S. 2018. Biology of viral satellites and their role in pathogenesis. Current Opinion in Virology 33: 96-105.
Grimsley N., Hohn B. and Hohn T. Walden R. 1986. Agroinfection, an alternative route for viral-infection of plants by using the Ti plasmid. Proceedings of the National Academy of Sciences, USA 83: 3282-3286.
Hamza M., Tahir M.N., Mustafa R., Kamal H., Khan M.Z., Mansoor S., Briddon R.W. and Amin I. 2018. Identification of a dicot infecting mastrevirus along with alpha-and betasatellite associated with leaf curl disease of spinach (Spinacia oleracea) in Pakistan. Virus Research 256: 174–182.
Holmes D.S. and Quigley M. 1981. A rapid boiling method for the preparation of bacterial plasmids. Analytical Biochemistry 114: 193-197.
Horn N.M., Reddy S.V., Roberts I.M. and Reddy D.V.R. 1993. Chickpea chlorotic dwarf virus, a new leafhopper transmitted geminivirus of chickpea in India. Annals of Applied Biology 122: 467–479.
Kanakala S. and Kuria P. 2018. Chickpea chlorotic dwarf virus: An emerging monopartite dicot infecting mastrevirus. Viruses 11(1).
Kraberger S., Kumari S.G., Hamed A.A., Gronenborn B., Thomas J.E., Sharman M., Harkins G.W., Muhire B.M., Martin D.P. and Varsani A. 2015. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination: a driving force in the emergence of new strains. Infection, Genetics and Evolution 29: 203–215.
Kumar J., Kumar J., Singh S.P. and Tuli R., 2014. Association of satellites with a mastrevirus in natural infection: complexity of wheat dwarf India virus disease. Journal of Virology 88: 7093-7104.
Kumar R., Palicherla S.R., Mandal B. and Kadiri S. 2018a. PCR based detection of betasatellite associated with the begomoviruses using improved universal primers. Australasian Plant Pathology 47: 115-118.
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.
Muhire B.M., Varsani A. and Martin D.P. 2014. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9 (9): e108277.
Navas-Castillo J. and Fiallo-Olivé E. 2021. Geminiviruses (Geminiviridae). pp 411–419. In: Encyclopedia of Virology, 4th ed., Vol. 3, Bamford D.H., Zuckerman M. (Eds.), Academic Press, Oxford, UK.
Roumagnac P., Lett J.M., Fiallo-Olivé E., Navas-Castillo J., Zerbini F.M., Martin D.P. and Varsani A. 2022. Establishment of five new genera in the family Geminiviridae: Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus. Archives of Virology 167(2): 695-710.
Salari Kh., Heydarnejad J., Massumi H. and Varsani A. 2023. Incidence of cotton leaf curl Gezira virus and the associated alphasatellites and betasatellites in crops and ornamental plants in southern Iran. Tropical Plant Pathology 48: 62-72.
Shahmohammadi N., Dizadji A., Bihamta M.R. and Kvarnheden A. 2020. Diversity and occurrence of chickpea chlorotic dwarf virus on legumes from Iran. Plant Pathology 69:139-148.
Shepherd D.N., Martin D.P., Lefeuvre P., Monjane A. L., Owor B.E., Rybicki E.P. and Varsani A. 2008. A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. Journal of Virological Methods 149: 97-102.
Zhang Y.P., Uyemoto J.K. and Kirkpatrick B.C. 1998. A small-scale procedure for extracting nucleic acids from woody plants infected with various phytopathogens for PCR assay. Journal of Virological Methods 71(1): 45-50.
Zia-Ur-Rehman M., Hameed U., Ali C.A., Haider M.S. and Brown J.K. 2017. First report of Chickpea chlorotic dwarf virus infecting okra in Pakistan. Plant Disease 101: 1336.
Iranian Journal of Plant Pathology
Volume 58, Issue 4
January 2024
Pages 218-230

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