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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #405441
Research Project: Identifying Vulnerabilities in Vector-host-pathogen Interactions of Grapevine and Citrus Pathosystems to Advance Sustainable Management Strategies

Location: Crop Diseases, Pests and Genetics Research

Title: Whole genome sequence of Citrus yellow vein clearing virus CA1 isolate

Author
item Sun, Yongduo
item Yokomi, Raymond - Ray

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/31/2023
Publication Date: 8/10/2023
Citation: Sun, Y., Yokomi, R.K. 2023. Whole genome sequence of Citrus yellow vein clearing virus CA1 isolate. BMC Research Notes. 16. Article 166. https://doi.org/10.1186/s13104-023-06443-7.
DOI: https://doi.org/10.1186/s13104-023-06443-7

Interpretive Summary: Citrus yellow vein clearing virus (CYVCV) is an emerging pathogen that poses a significant threat to the citrus industry in California. The virus distribution is limited to urban citrus trees in the cities of Tulare and Visalia, and to date, has not been found in any commercial citrus orchards in the United States. The genome of this virus, CYVCV CA1 isolate was sequenced, annotated, and compared with other known CYVCV from abroad. Phylogenetic anyalsis suggest that this virus was most closely related to a CYVCV isolate from India. This information is important for regulatory agencies to identify the potential port of entry of this exotic virus.

Technical Abstract: Citrus yellow vein clearing virus (CYVCV) is an emerging pathogen that poses a significant threat to the citrus industry in California. In this study, the viral genomic RNA was isolated from Eureka lemon plants in the greenhouse exhibiting symptoms of CYVCV. Subsequently, the corresponding DNA genome amplicon was sequenced and annotated. These efforts expand the genotype database of CYVCV, which aim to enhance detection assays, promote understanding of the virus's genetics and evolution, and ultimately support disease management. In this report, the complete genome sequence of the CYVCV California isolate (CA1) is reported. The genome was found to be 7,530 bp in length, with a G+C content of 51.7%. The 5' and 3' termini were determined using 5' and 3' termini rapid amplification of cDNA ends (RACE) systems. Furthermore, our analysis revealed the presence of six open reading frames (ORFs) potentially encoding proteins. All sequence data and annotation have been deposited in GenBank under the accession number OR037276.