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ARS Home » Southeast Area » Auburn, Alabama » Soil Dynamics Research » Research » Publications at this Location » Publication #413174
Research Project: Integrated Crop Disease Mitigation through Improved Understanding of Relationships between Genetics, Environment, and Management

Location: Soil Dynamics Research

Title: Cotton contains multitudes: A metatranscriptomics sequencing approach reveals the cotton virome in the southern United States

Author
item ESCALANTE, CESAR - Auburn University
item REYES, ANYI - Auburn University
item Zhao, Chaoyang
item JACOBSON, ALANA - Auburn University
item Balkcom, Kipling
item CONNER, KASSIE - Auburn University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/25/2025
Publication Date: 3/6/2025
Citation: Escalante, C., Reyes, A.M., Zhao, C., Jacobson, A., Balkcom, K.S., Conner, K. 2025. Cotton contains multitudes: A metatranscriptomics sequencing approach reveals the cotton virome in the southern United States [abstract]. Phytopathology 114:S1.28. https://doi.org/10.1094/PHYTO-114-11-S1.1.
DOI: https://doi.org/10.1094/PHYTO-114-11-S1.1

Interpretive Summary:

Technical Abstract: High-throughput sequencing techniques have revolutionized the discovery and characterization of viruses. In the U.S., virologists have scrutinized cotton leafroll dwarf virus (CLRDV) since its recent discovery in cotton-producing states. However, yield loss has been sporadically observed, suggesting specific factors are responsible for yield loss outcomes. This study aimed to characterize the cotton virome and determine if mixed viral infections are present in cotton. A total of 51 leaf samples were collected from Alabama, Florida, Georgia, Louisiana, North Carolina, and South Carolina in 2021. Total RNA was extracted, and libraries were sequenced in an Illumina platform. A total of 336 viral contigs were de novo assembled. Approximately 54 sequences were characterized as full genomes. Full contigs of CLRDV were detected from all samples analyzed. Putative sequences with the highest relative abundance included members of the viral families Botourmiaviridae, Leviviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, Totiviridae. Four putative virus species in the families Solemoviridae, Mitoviridae, Botourmiaviridae, and Leviviridae were selected for RT-PCR validation. PCR products with expected sizes were obtained from all four species, and their sequences were also validated by Sanger sequencing. These results expand our understanding of the abundance and diversity of viruses in cotton agroecosystems and provide a foundation for future studies to better characterize viruses with potential economic importance in cotton.