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Genome characterization of fig umbra-like virus

Abstract

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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Acknowledgements

Funding was provided by National Institute of Food and Agriculture (Hatch HAW09025-H[1001478]), 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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XW, AO-V, and MM performed experiments. XW, AO-V, AES, and MM performed data analysis. XW and AO-V wrote the manuscript. AO-V, JH, and MM designed experiments. JH and MM supervised the study. All authors contributed to the review and modification of the manuscript.

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Correspondence to John Hu or Michael Melzer.

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The authors declare that they have no conflicts of interest.

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This study did not include experiments with human or animal participants performed by any of the authors.

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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

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Keywords

  • Umbra-like virus
  • Fig
  • Hawaii
  • New species
  • High-throughput sequencing