Abstract
A new virus was identified in a celery plant showing chlorotic rings, mosaic and strong yellowing symptoms, and its complete genome sequence was determined. The genomic organization of this novel virus is analogous to that of known members of the genus Torradovirus, consisting of two single-stranded RNAs of 6,823 (RNA1) and 4,263 nucleotides (RNA2), excluding the poly(A) tails. BLAST searches against the nucleotide and protein databases showed that this virus is closely related to but different from carrot torradovirus 1 (CaTV1). Comparisons between the two viruses demonstrated relatively low levels of nucleotide and amino acid similarity in different parts of their genomes, as well as considerable differences in the sizes of their two genomic RNAs. However, the protease-polymerase (Pro-Pol) and capsid protein (CP) regions of this virus share >80% amino acid identity with the corresponding regions of CaTV1. Therefore, based on the current ICTV species demarcation criteria for the family Secoviridae, the virus from celery is a divergent strain of CaTV1, named “CaTV1-celery”. Nevertheless, differences between CaTV1 and CaTV1-celery in genome size, as well as in biological and epidemiological features, may warrant their separation into two distinct species in the future.
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References
Coutts RHA, Livieratos IC (2003) A rapid method for sequencing the 5’- and 3’-termini of double-stranded RNA viral templates using RLM-RACE. J Phytopathol 151(9):525–527. https://doi.org/10.1046/j.1439-0434.2003.00755.x
Untergasser A, Cutcutache I, Koressaar T et al (2012) Primer3–new capabilities and interfaces. Nucleic Acids Res 40(15):e115. https://doi.org/10.1093/nar/gks596
Sanfaçon H, Wellink J, Le Gall O et al (2009) Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch Virol 154(5):899–907. https://doi.org/10.1007/s00705-009-0367-z
Thompson JR, Dasgupta I, Fuchs M et al (2017) ICTV virus taxonomy profile: Secoviridae. J Gen Virol 98(4):529–531. https://doi.org/10.1099/jgv.0.000779
Gorbalenya AE, Koonin EV, Donchenko AP et al (1989) Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17(12):4713–4730
Gorbalenya AE, Snijder EJ (1996) Viral cysteine proteinases. Perspect Drug Discov Des 6(1):64–86. https://doi.org/10.1007/BF02174046
Argos P, Kamer G, Nicklin MJ et al (1984) Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Res 12(18):7251–7267
Mushegian AR (1994) The putative movement domain encoded by nepovirus RNA-2 is conserved in all sequenced nepoviruses. Arch Virol 135(3–4):437–441. https://doi.org/10.1007/BF01310028
Verbeek M, Dullemans AM, van den Heuvel JFJM et al (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152(5):881–890. https://doi.org/10.1007/s00705-006-0917-6
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. https://doi.org/10.1093/molbev/msw054
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and clustal X version 2.0. Bioinformatics 23(21):2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Verbeek M, Dullemans AM, van der Vlugt RAA (2017) Aphid transmission of Lettuce necrotic leaf curl virus, a member of a tentative new subgroup within the genus Torradovirus. Virus Res 241:125–130. https://doi.org/10.1016/j.virusres.2017.02.008
Rozado-Aguirre Z, Adams I, Collins L et al (2016) Detection and transmission of carrot torrado virus, a novel putative member of the Torradovirus genus. J Virol Methods 235:119–124. https://doi.org/10.1016/j.jviromet.2016.05.018
Verbeek M, Dullemans A, van den Heuvel H et al (2010) Tomato chocolàte virus: a new plant virus infecting tomato and a proposed member of the genus Torradovirus. Arch Virol 155(5):751–755. https://doi.org/10.1007/s00705-010-0640-1
Acknowledgements
The authors thank Ms. Roswitha Ulrich for providing the original sample. The authors are grateful to Ms. Angelika Sieg-Müller, Ms. Petra Lüddecke, Ms. Kerstin Herz and Mr. Jonas Hartrick for their outstanding technical assistance, and Mr. Christopher Ziebell for proofreading.
Funding
This research was financed by EUPHRESCO (2015-F-172) project “The Application of Next-Generation Sequencing Technology for the Detection and Diagnosis of Non-culturable Organisms: Viruses and viroids”. Yahya Z. A. Gaafar was supported by a German Egyptian Research Long Term Scholarship.
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Gaafar, Y.Z.A., Ziebell, H. Complete genome sequence of a highly divergent carrot torradovirus 1 strain from Apium graveolens. Arch Virol 164, 1943–1947 (2019). https://doi.org/10.1007/s00705-019-04272-3
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DOI: https://doi.org/10.1007/s00705-019-04272-3