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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #380988

Research Project: Genetic Improvement and Sustainable Production Systems for Sub-tropical and Tropical Crops in the Pacific Basin

Location: Tropical Plant Genetic Resources and Disease Research

Title: Genome characterization of fig umbra-like virus

Author
item WANG, X - University Of Hawaii
item OLMEDO-VELARDE, A - University Of Hawaii
item LARREA-SARMIENTO, A - University Of Hawaii
item KONG, A - University Of Hawaii
item BORTH, W - University Of Hawaii
item Suzuki, Jon
item Wall, Marisa
item HU, JOHN - University Of Hawaii
item MELZER, MICHAEL - University Of Hawaii

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2021
Publication Date: 9/15/2021
Citation: Wang, X., Olmedo-Velarde, A., Larrea-Sarmiento, A., Kong, A., Borth, W., Suzuki, J.Y., Wall, M.M., Hu, J.S., Melzer, M. 2021. Genome characterization of fig umbra-like virus. Virus Genes. https://doi.org/10.1007/s11262-021-01867-4.
DOI: https://doi.org/10.1007/s11262-021-01867-4

Interpretive Summary: Edible fig (Ficus carica) is a crop that is primarily propagated by cuttings and thus prone to the accumulation of viral pathogens. Fig mosaic disease (FMD) is a complex syndrome of putative viral origin that has been commonly reported in areas where fig is grown. Typical symptoms of FMD are foliar chlorosis, deformation, and mosaic patterning. From prior studies, researchers have identified 12 plant viruses and three plant virus-like pathogens from fig trees displaying these symptoms. In this study, modern sequencing techniques were used to identify the entire genome of yet a new plant virus, named in this study “fig umbra-like virus” from fig trees exhibiting disease symptoms. Identifying and tracking the different viruses infecting fig will help to understand how to control plant virus-caused disease emergence and spread in this important agricultural crop.

Technical Abstract: The complete genome of a new umbra-like virus from edible fig (Ficus carica) was identifed 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 mono-phyletic 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.