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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Publications at this Location » Publication #405826

Research Project: Management and Biology of Arthropod Pests and Arthropod-borne Plant Pathogens

Location: Emerging Pests and Pathogens Research

Title: Characterization of cotton virus A, a distinct member of the caulimovirus genus with endogenous viral elements in upland cotton

item WEST-ORTIZ, MICHAEL - Cornell University
item STUEHLER, DOUGLAS - Oak Ridge Institute For Science And Education (ORISE)
item POLLOCK, EMMA - Cornell University
item Wilson, Jennifer - Jenny
item PREISING, STEPHANIE - Cornell University
item ALABI, OLUFEMI - Texas A&M University
item FUCHS, MARK - Cornell University
item Heck, Michelle
item OLMEDO-VELARDE, ALEJANDRO - Cornell University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 6/14/2023
Publication Date: 6/14/2023
Citation: West-Ortiz, M., Stuehler, D., Pollock, E., Wilson, J.R., Preising, S., Alabi, O., Fuchs, M., Heck, M.L., Olmedo-Velarde, A. 2023. Characterization of cotton virus A, a distinct member of the caulimovirus genus with endogenous viral elements in upland cotton. bioRxiv.

Interpretive Summary: The United States (US) is the world’s third largest producer and the leader in cotton exports. A current threat to the cotton industry is cotton blue disease, caused by the RNA virus, cotton leafroll dwarf virus (CLRDV). CLRDV has spread to most cotton-producing states throughout the cotton belt. Since plants infected with CLRDV do not always display symptoms, there was a need to determine if additional viruses are present in CLRDV-infected plants. Using molecular and computational tools, ARS scientists in partnership with university cooperators discovered a new DNA virus infecting cotton growing in Mississippi and characterized the complete virus genome. The new virus is tentatively named cotton virus A (CotV-A). Similar to other DNA plant viruses and using computational approaches, the team also discovered copies of the CotV-A genome inserted into the genome of upland cotton and a few wild relatives. Further research is ongoing to determine whether CotV-A can cause detrimental effects in cotton production, if the virus copies inserted in the upland cotton genome can initiate a real virus infection or whether the virus is transmitted by insects.

Technical Abstract: The complete genome sequence of cotton virus A (CotV-A), a new virus infecting cotton (Gossypium spp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other species in the genus Caulimovirus (family Caulimoviridae) but with key genome organization differences. Although P3, P5 and P6 are presumed movement, coat and reverse transcriptase proteins, respectively, P1, P2 and P4 showed no sequence homology to any virus protein. Endogenous virus elements were found in available genomic data for G.hirsutum and G. tomentosum, but not in G. barbadense, G. arboreum, or G. herbaceum.