Abstract
Faba bean necrotic stunt virus (FBNSV) (genus Nanovirus; family Nanoviridae) is a multipartite virus comprising eight circular single-stranded DNA components, each about 1 kb in length. Also, two alphasatellites have often been reported to be associated with FBNSV infection. The only full-length genome sequence of an Iranian FBNSV isolate, FBNSV-[IR;Ka:FB], so far reported is one infecting faba bean (Vicia faba L.). To obtain more information about Iranian isolates of FBNSV (FBNSV-IRs) and their diversity, the full-length genome of four FBNSV isolates and associated alphasatellites obtained from faba bean (two isolates), common bean (Phaseolus vulgaris L., one isolate) and chickpea (Cicer arietinum L., one isolate) were characterized. All genomic components except U4 had the expected size in accordance with the FBNSV genomic sequences published in the GenBank. The component U4 had an additional stretch of 16 nucleotides (nts 765–780) in its non-coding region (NCR). Alphasatellites of the aforementioned isolates showed 98–100% sequence identity. Intra-component sequence analyses of FBNSV-IRs indicated a range of 98 to 100% nt identity between each single FBNSV-IRs component or between their associated alphasatellites. DNA-M and DNA-U2 exhibited the highest value of diversity, sharing 98–99% identity. Phylogenetic analyses indicated that FBNSV-IRs were clustered with a Moroccan isolate and some Azerbaijani isolates of FBNSV forming a clade distinct from Ethiopian isolates. Inter-component sequence analyses of NCRs revealed the DNA-S and DNA-U4 subgrouped together in all FBNSV-IRs isolates except the chickpea isolate in which NCRs of DNA-S and DNA–U4 formed separate subgroups.
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References
Abraham, A. D., Varrelmann, M., & Vetten, H. J. (2012). Three distinct nanoviruses, one of which represents a new species, infect faba bean in Ethiopia. Plant Disease, 96(7), 1045–1053.
Abraham, A. D., Bencharki, B., Torok, V., Katul, L., Varrelmann, M., & Vetten, H. J. (2010). Two distinct nanovirus species infecting faba bean in Morocco. Archives of Virology, 155(1), 37–46.
Al-Nsour, A., Mansour, A., Al-Musa, A., & Salem, N. (1998). Distribution and incidence of faba bean necrotic yellows virus in Jordan. Plant Pathology, 47(4), 510–515.
Alavinejad, E., Behjatnia, S. A. A., Izadpanah, K., & Masoumi, M. (2011). Molecular detection of faba bean necrotic yellows virus in legume fields of some north, northwest and south provinces of Iran. The 7th National Biotechnology Congress of Iran.
Babin, M., Ortíz, V., Castro, S., & Romero, J. (2000). First detection of faba bean necrotic yellow virus in Spain. Plant Disease, 84(6), 707.
Bahrami, O., Alavinejad, E., Behjatnia, S. A. A., & Izadpanah, K. (2018). Genetic, host and geographical diversity of bean leaf roll virus, faba bean necrotic yellows virus and faba bean necrotic stunt virus in Iran. Proceedings of Iranian Plant Protection Congress, 606–607.
Briddon, R. W., Martin, D. P., Roumagnac, P., Navas-Castillo, J., Fiallo-Olivé, E., Moriones, E., et al. (2018). Alphasatellitidae: A new family with two subfamilies for the classification of geminivirus-and nanovirus-associated alphasatellites. Archives of Virology, 163(9), 2587–2600.
Burns, T. M., Harding, R. M., & Dale, J. L. (1995). The genome organization of banana bunchy top virus: Analysis of six ssDNA components. Journal of General Virology, 76(6), 1471–1482.
Chu, P. W. G., & Helms, K. (1988). Novel virus-like particles containing circular single-stranded DNAs associated with subterranean clover stunt disease. Virology, 167(1), 38–49.
Edgar, R. C. (2004). MUSCLE : Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797.
El-Muadhidi, M. A., Makkouk, K. M., Kumari, S. G., Jerjess, M., Murad, S. S., Mustafa, R. R., & Tarik, F. (2001). Survey for legume and cereal viruses in Iraq. Phytopathologia Mediterranea, 40(3), 224–233.
Gaafar, Y., Grausgruber-Gröger, S., & Ziebell, H. (2016). Vicia faba, V. sativa and Lens culinaris as new hosts for pea necrotic yellow dwarf virus in Germany and Austria. New Disease Reports, 34, 28.
Gaafar, Y., Timchenko, T., & Ziebell, H. (2017). First report of Pea necrotic yellow dwarf virus in the Netherlands. New Disease Reports, 35, 23.
Gallet, R., Kraberger, S., Filloux, D., Galzi, S., Fontes, H., Martin, D. P., et al. (2018). Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhône delta region of France. Archives of Virology, 163(3), 695–700.
Gawel, N. J., & Jarret, R. L. (1991). A modified CTAB DNA extraction procedure for Musa and ipomoea. Plant Molecular Biology Reporter, 9(3), 262–266.
Ghosh, A., Das, A., Vijayanandraj, S., & Mandal, B. (2015). Cardamom bushy dwarf virus infection in large cardamom alters plant selection preference, life stages, and fecundity of aphid vector, Micromyzus kalimpongensis (Hemiptera: Aphididae). Environmental Entomology, 45(1), 178–184.
Grigoras, I., del Cueto Ginzo, A. I., Martin, D. P., Varsani, A., Romero, J., Mammadov, A. C., et al. (2014). Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe. Journal of General Virology, 95(5), 1178–1191.
Grigoras, I., Timchenko, T., Grande-Perez, A., Katul, L., Vetten, H. J., & Gronenborn, B. (2010). High variability and rapid evolution of a nanovirus. Journal of Virology, 84(18), 9105–9117.
Grigoras, I., Timchenko, T., Katul, L., Grande-Perez, A., Vetten, H. J., & Gronenborn, B. (2009). Reconstitution of authentic nanovirus from multiple cloned DNAs. Journal of Virology, 83(20), 10778–10787.
Hema, M., Sreenivasulu, P., Patil, B. L., Kumar, P. L., & Reddy, D. V. (2014). Tropical food legumes: Virus diseases of economic importance and their control. Advances in Virus Research, 90, 431–505.
Heydarnejad, J., Kamali, M., Massumi, H., Kvarnheden, A., Male, M. F., Kraberger, S., et al. (2017). Identification of a nanovirus-alphasatellite complex in Sophora alopecuroides. Virus Research, 235, 24–32.
Hooks, C. R., Fukuda, S., Perez, E. A., Manandhar, R., Wang, K. H., Wright, M. G., & Almeida, R. P. (2009). Aphid transmission of banana bunchy top virus to bananas after treatment with a bananacide. Journal of Economic Entomology, 102(2), 493–499.
Horser, C. L., Harding, R. M., & Dale, J. L. (2001a). Banana bunchy top nanovirus DNA-1 encodes the “master” replication initiation protein. Journal of General Virology, 82(2), 459–464.
Horser, C. L., Karan, M., Harding, R. M., & Dale, J. L. (2001b). Additional rep-encoding DNAs associated with banana bunchy top virus. Archives of Virology, 146(1), 71–86.
Katul, L., Maiss, E., Morozov, S. Y., & Vetten, H. J. (1997). Analysis of six DNA components of the faba bean necrotic yellows virus genome and their structural affinity to related plant virus genomes. Virology, 233(2), 247–259.
Katul, L., Timchenko, T., Gronenborn, B., & Vetten, H. J. (1998). Ten distinct circular ssDNA components, four of which encode putative replication-associated proteins, are associated with the faba bean necrotic yellows virus genome. Journal of General Virology, 79(12), 3101–3109.
Kraberger, S., Kumari, S. G., Najar, A., Stainton, D., Martin, D. P., & Varsani, A. (2018). Molecular characterization of faba bean necrotic yellows viruses in Tunisia. Archives of Virology, 163(3), 687–694.
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7 : Molecular evolutionary genetics analysis version 7.0 for bigger datasets brief communication. Molecular Biology and Evolution, 33(7), 1870–1874.
Kumari, S. G., Attar, N., Mustafayev, E., & Akparov, Z. (2009). First report of Faba bean necrotic yellows virus affecting legume crops in Azerbaijan. Plant Disease, 93(11), 1220.
Lotfipour, M., Izadpanah, K., & Behjatnia, S. A. A. (2017). Identification and molecular characterization of Faba bean necrotic stunt virus, a new nanovirus in legume fields in Iran. Iranian Journal of Plant Pathology, 52(4), 503–517.
Makkouk, K. M., Fazlali, Y., Kumari, S. G., & 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(3), 387.
Makkouk, K. M., Hamed, A. A., Hussein, M., & Kumari, S. G. (2003). First report of Faba bean necrotic yellows virus ( FBNYV ) infecting chickpea (Cicer arietinum) and faba bean (Vicia faba) crops in Sudan. Plant Pathology, 52(3), 412.
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.
Ortiz, V., Navarro, E., Castro, S., Carazo, G., & Romero, J. (2006). Incidence and transmission of Faba bean necrotic yellows virus ( FBNYV ) in Spain. Spanish Journal of Agricultural Research, 4(3), 255–260.
Sano, Y., Wada, M., Hashimoto, Y., Matsumoto, T., & Kojima, M. (1998). Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome. Journal of General Virology, 79(24), 3111–3118.
Saunders, K., & Stanley, J. (1999). A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: Evidence for interfamilial recombination between plant DNA viruses. Virology, 264(1), 142–152.
Sharman, M., Thomas, J. E., Skabo, S., & Holton, T. A. (2008). Abacá bunchy top virus, a new member of the genus Babuvirus (family Nanoviridae). Archives of Virology, 153(1), 135–147.
Stainton, D., Kraberger, S., Walters, M., Wiltshire, E. J., Rosario, K., Lolohea, S., et al. (2012). Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. Journal of General Virology, 93(5), 1103–1119.
Timchenko, T., De Kouchkovsky, F., Vetten, H. J., & Gronenborn, B. (1999). A single rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants. Journal of Virology, 73(12), 10173–10182.
Timchenko, T., Katul, L., Sano, Y., De Kouchkovsky, F., Vetten, H. J., & Gronenborn, B. (2000). The master rep concept in nanovirus replication: Identification of missing genome components and potential for natural genetic reassortment. Virology, 274(1), 189–195.
Vetten, H. J., Dale, J. L., Grigoras, I., Gronenborn, B., Harding, R., Randles, J. W., et al. (2012). Family Nanoviridae. In A. M. Q. King, M. J. Adams, E. B. Carsten, & E. J. Lefkowitz (Eds.), Virus taxonomy, classification and nomenclature of viruses. Ninth report of the international committee on taxonomy of viruses (pp. 395–404). Amsterdam: Elsevier.
Vetten, H. J., Knierim, D., Rakoski, M., Menzel, S., Maiss, W., Gronenborn, E., Winter, S. B., & Krenz, B. (2019). Identification of a novel nanovirus in parsley. Archives of Virology, 164(7), 1883–1887.
Watanabe, S., Greenwell, A., & Bressan, A. (2013). Localization, concentration, and transmission efficiency of banana bunchy top virus in four asexual lineages of Pentalonia aphids. Viruses, 5(2), 758–776.
Acknowledgments
Maedeh Lotfipour was financially supported by Shiraz University, Shiraz, Iran and University of Bologna, Italy. We thank Professor Keramat Izadpananh from Shiraz University, Shiraz, Iran and Professor Jahangir Heydarnejad from Shahid Bahonar University of Kerman, Kerman, Iran for careful reading of the manuscript.
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Lotfipour, M., Behjatnia, S.A.A., Dall’Ara, M. et al. The full-length genome characterization and diversity of faba bean necrotic stunt virus in Iran. Eur J Plant Pathol 157, 239–250 (2020). https://doi.org/10.1007/s10658-020-01973-3
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DOI: https://doi.org/10.1007/s10658-020-01973-3