The complete genome of a new umbra-like virus from edible fig (Ficus carica) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus Umbravirus, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family Tombusviridae.
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Lim S, Lee S-H, Moon JS (2019) Complete genome sequence of a tentative new umbravirus isolated from Patrinia scabiosaefolia. Arch Virol 164(9):2375–2378. https://doi.org/10.1007/s00705-019-04312-y
Yoo RH, Lee S-W, Lim S, Zhao F, Igori D, Baek D, Hong J-S, Lee S-H, Moon JS (2017) Complete genome analysis of a novel umbravirus-polerovirus combination isolated from Ixeridium dentatum. Adv Virol 162(12):3893–3897. https://doi.org/10.1007/s00705-017-3512-0
Ryabov EV, Taliansky ME, Robinson DJ, Waterhouse PM, Murant AF, de Zoeten GA, Falk BW, Vetten HJ, Gibbs MJ (2012) Umbravirus. In: King AM, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy. Ninth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, London, pp 1191–1195
Quito-Avila DF, Alvarez R, Ibarra M, Martin R (2015) Detection and partial genome sequence of a new umbra-like virus of papaya discovered in Ecuador. Eur J Plant Pathol 143(1):199–204. https://doi.org/10.1007/s10658-015-0675-y
Sá Antunes TF, Amaral RJV, Ventura JA, Godinho MT, Amaral JG, Souza FO, Zerbini PA, Zerbini FM, Fernandes PMB (2016) The dsRNA virus papaya meleira virus and an ssRNA virus are associated with papaya sticky disease. PLos One 11(5):e0155240. https://doi.org/10.1371/journal.pone.0155240
Tahir MN, Bolus S, Grinstead SC, McFarlane SA, Mollov D (2021) A new virus of the family Tombusviridae infecting sugarcane. Adv Virol 166(3):961–965. https://doi.org/10.1007/s00705-020-04908-9
Felker P, Bunch R, Russo G, Preston K, Tine JA, Suter B, Xiaohan M, Cushman JC, Yim WC (2019) Biology and chemistry of an Umbravirus like 2989 bp single stranded RNA as a possible causal agent for Opuntia stunting disease (engrosamiento de cladodios)-A Review. J Prof Assoc Cactus Dev 21:1–31
Kwon S-J, Bodaghi S, Dang T, Gadhave KR, Ho T, Osman F, Al Rwahnih M, Tzanetakis IE, Simon AE, Vidalakis G (2021) Complete nucleotide sequence, genome organization and comparative genomic analyses of citrus yellow-vein associated virus (CYVaV). Front Microbiol 12:683130. https://doi.org/10.3389/fmicb.2021.683130
Preising S, Borges D, Ambrosio MMQ, da Silva WL (2020) A fig deal: A global look at fig mosaic disease and its putative associates. Plant Dis 105(4):727–738. https://doi.org/10.1094/PDIS-06-20-1352-FE
Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE (2019) High throughput sequencing for plant virus detection and discovery. Phytopathology 109(5):716–725. https://doi.org/10.1094/PHYTO-07-18-0257-RVW
Perez-Losada M, Arenas M, Galan JC, Bracho MA, Hillung J, Garcia-Gonzalez N, Gonzalez-Candelas F (2020) High-throughput sequencing (HTS) for the analysis of viral populations. Infect Genet Evol 80:104208. https://doi.org/10.1016/j.meegid.2020.104208
Olmedo-Velarde A, Park AC, Sugano J, Uchida JY, Kawate M, Borth WB, Hu JS, Melzer MJ (2019) Characterization of Ti Ringspot-associated virus, a Novel Emaravirus associated with an emerging Ringspot disease of Cordyline Fruticosa. Plant Dis 103(9):2345–2352. https://doi.org/10.1094/PDIS-09-18-1513-RE
Zhang J, Dey KK, Lin B, Borth WB, Melzer MJ, Sether D, Wang Y, Wang I-C, Shen H, Pu X, Sun D, Hu JS (2017) Characterization of Canna yellow mottle virus in a New Host, Alpinia purpurata, in Hawaii. Phytopathol 107(6):791–799. https://doi.org/10.1094/PHYTO-04-16-0160-R
Wang Y, Wu B, Borth WB, Hamim I, Green JC, Melzer MJ, Hu JS (2017) Molecular characterization and distribution of two strains of Dasheen mosaic virus on Taro in Hawaii. Plant Dis 101(12):1980–1989. https://doi.org/10.1094/PDIS-04-17-0516-RE
Liu J, Carino E, Bera S, Gao F, May JP, Simon AE (2021) Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs. Viruses 13(4):646. https://doi.org/10.3390/v13040646
Gao F, Simon AE (2016) Multiple cis-acting elements modulate programmed-1 ribosomal frameshifting in Pea enation mosaic virus. Nucleic Acids Res 44(2):878–895. https://doi.org/10.1093/nar/gkv1241
Stecher G, Tamura K, Kumar S (2020) Molecular evolutionary genetics analysis (MEGA) for macOS. Mol Biol Evol 37(4):1237–1239. https://doi.org/10.1093/molbev/msz312
Chomič A, Pearson M, Clover G, Farreyrol K, Saul D, Hampton J, Armstrong K (2010) A generic RT-PCR assay for the detection of Luteoviridae. Plant Pathol 59(3):429–442. https://doi.org/10.1111/j.1365-3059.2010.02282
Kozak M, Shatkin AJ (1978) Identification of features in 5′ terminal fragments from reovirus mRNA which are important for ribosome binding. Cell 13(1):201–212. https://doi.org/10.1016/0092-8674(78)90150-2
Funding was provided by National Institute of Food and Agriculture (Hatch HAW09025-H), Agricultural Research Service (58-5320-4-012), and United States Agency for International Development (BFS-G-1100002 and EEM-G-0004-00013) to JH. Funding was also provided from National Science Foundation MCB-1818229 and United States Department of Agriculture: The NIFA Citrus Disease Research and Extension grant AP18PPQS&T00C223 program to AES.
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Edited by Seung-Kook Choi.
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Wang, X., Olmedo-Velarde, A., Larrea-Sarmiento, A. et al. Genome characterization of fig umbra-like virus. Virus Genes 57, 566–570 (2021). https://doi.org/10.1007/s11262-021-01867-4
- Umbra-like virus
- New species
- High-throughput sequencing