Phylogeny, genetic diversity and population structure of Faba bean necrotic yellows virus based on the nucleotide sequence of DNA-M

Document Type : Research Article

Authors

Faculty member

Abstract

Faba bean necrotic yellows virus (FBNYV) causes severe yield losses and crop failure in legumes in the north African, south Asian and European countries. Following nucleotide sequencing of DNA-M segment of 17 host and geographical FBNYV isolates in Iran, different molecular analysis were performed based on all available DNA-M sequences of FBNYV. Based on constructed phylogenetic tree using nucleotide sequence of DNA-M component, FBNYV isolates were grouped into three clades, including isolates from Iran and Azerbaijan as a distinct clade. Genetic distance studies of FBNYV host subpopulations revealed some evidences of host adaptation in FBNYV natural selection. High gene flow was found among Iran – Azerbaijan and Spain – Africa subpopulations, indicating the relationship of their origins. Maximum genetic diversity of DNA-M was estimated in the central subpopulation of Iran. The dN/dS (Ѡ) value less than 1 represented the negative selection pressure on the movement protein of the virus. Seven out of nine recombination events were detected in DNA-M of Iranian FBNYV isolates. This is the first report of the FBNYV infection on pea from Iran. In the current study, the complete DNA-M nucleotide sequences of French bean and pea isolates of FBNYV were determined for the first time in the world.

Keywords


Alavinejad E., Behjatnia S. A. A., Izadpanah K. and Masoumi M. (2011). Molecular detection of Faba bean necrotic yellows virus in legume fields of some
North, North West and South provinces of Iran. The 7th National Biotechnology Congress of I. R. Iran. 6 pp. (in Persian with English summary).
Anonymous. (2018). Statistical annual report of Iranian agricultural crops. (In Persian)
Asghari G. S., Shahraeen N., Ghorbani S. and Hosseinnia S. (2009). Identification of Faba bean necrotic yellows virus in Mazandaran province, Iran. Indian Journal of Virology 20: 11-13.
Alberter B., Rezaian A. M., Jeske H. (2005). Replicative intermediates of ToLCV and its satellite DNAs. Virology 331: 441–448.
Elena S. F. 2017. Local adaptation of plant viruses: lessons from experimental evolution. Molecular Ecology 26 (7): 1711-1719.
El- muadhidi M. A., Makkouk K. M., Kumari S. G., Jerjess M., Murad S. S., Mustafa R. R. and Tarik F. (2001). Survey for legume and cereal viruses in Iraq. Phytopathologia Mediterranea 40: 224-233.
Escrui F. (2017). Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies. In: Bits L. (Ed). Genetic diversity. InTech. Rijeca. 3-18.
Faraji K., Farzadfar Sh., Maleki M. and Pour Rahim R. (2012). Application of PCR to detect Faba bean necrotic yellows virus in Alfalfa fields of Ilam province. 12th Congress of Iranian Genetics Society. Tehran.
Franz A. W. E., Wilk F. V. D., Verbeek M., Dullemans A. M. and Heuvel J. F. J. M. (1999). Faba bean necrotic yellows virus (Genus Nanovirus) requires a helper factor for its aphid transmission. Virology 29: 210-219.
Grigoras I., Timchenko T., Katul L., Grande-Prez A., Vetten H. G. and Gronenborn B. (2009). Reconstitution of authentic nanovirus from multiple cloned DNAs. Journal of Virology 83: 10778-10787.
Grigoras I., Timchenko T., Grande-perez A., Katul L., Vetten H. J and Gronenborn B. (2010). High variability and rapid evolution of a nanovirus. Journal of Virology 84(18): 9105-9117.
Grigoras I., del Cueto Ginzo A. I., Martin D. P., Varsani A., Romero J., Mammadov A. Ch., Aliyev J. A., Kheyr-Pour A., Huss H., Ziebell H., Timchenko T., Vetten H. J. and Gronenborn B. (2014). Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe. Journal of General Virology 95: 1178-1191.
Hull R. (2014). Plant virology (5th Edition). Academic Press, USA. 1056 p.
Karan M., Harding R. M. and Dale J. L. (1995). Evidence for two groups of banana bunchy top virus isolates. Journal of General Virology 75(12): 3541-6.
Kumari, S. G., Attar N., Mustafayev E. and Akparov Z. (2009). First report of Faba bean necrotic yellows virus affecting legume crops in Azerbaijan. Plant Disease 93: 1220.
Lefeuvre P., Lett J., M. , Varsani A. and Martin D. P. ( 2009 ). Widely conserved recombination patterns among single-stranded DNA viruses. Journal of Virology 83: 2697––2707. 
Libardo P. and Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Majnoon Hoseini N. (1995). Legumes in Iran. Academic center of education culture and research. University of Tehran. Iran. 284 p. (in Persian)
Makkouk K. M., Faslali Y., Kumari S. G. and Farzadfar S. (2002). First record of Beet western yellows virus, chickpea chlorotic dwarf virus, Faba bean necrotic yellows virus and soybean dwarf virus infecting chickpea and lentil crops in Iran. Plant Pathology 51: 387.
Makkouk K. M. and Kumari S. G. (2009). Epidemiology and integrated management of persistently transmitted aphid-borne viruses of legumes and cereal crops in West Asia and North Africa. Virus Research 141: 209-218.
Makkouk K. M., Pappu H. and Kumari S. G. (2012). Virus disease of peas, beans and faba bean in the Mediterranean Region. Advances in Virus Research 84: 367-402.
Marco C. F., Aranda M. A. (2005). Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus. Journal of General virology 88: 815-822.
Martin D.P., Murrell B., Golden M., Khoosal A. and Muhire B. (2015). RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution 1(1): 1-5.
Matsumura E. E., Filho H. D. C., Dorta S. O., Nouri Sh. and Machato M. A. (2016). Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil. Viruses 8: 330.
Nei M. (1987). Molecular Evolutionary Genetics. Columbia university press. 512 p.
Ortiz A., Navarro E., Castro S., Carazo G. and Romero J. (2006). Incidence and transmission of Faba bean necrotic yellows virus (FBNYV) in Spain. Journal of Agricultural Research 4: 255-260.
Savory F. R., Varma V. and Ramkrishnan U. (2014). Identifying geographic hot spots of reassortment in a multipartite plant virus. Evolutionary Applications 7: 569-579.
Seal S. E., VandenBosch F. and Jeger M. J. (2006). Factors influencing begomovirus evolution and their increasing global significance: implication for sustainable control. Critical reviews in plant sciences 25(1): 23-46.
Sokhansanj Y., Bananej K., Rakhshandehroo F. and Ahoonmanesh A. (2018). Molecular characterization of three Faba bean necrotic yellows virus (FBNYV)
isolates, originated from chickpea in Iran. Entomology and Phytopathology 86(1): 77-90. (In Persian with English summary)
Stainton D., Kraberger S., Walters M., Wiltshire E. J., Rosario K., Halafihi M., Lolohea S., Katoa I., Faitua T. H., Aholelei W., Taufa L., Thomas J. E., Collings D. A., Martin D. P. and Varsani A. (2012) Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. Journal of General Virology 93: 1103-1119.
Tamura K., Stecher G., Peterson D., Filipski A. and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729.
Zhang Y., Vyomoto J. K. and Kirkpatrick B. C. (1998). A small-scale procedure for extracting nucleic acids from woody plants infected with various phytopathogenes for PCR assay. Journal of Virological Methods 71: 45-30.