Metatranscriptomics analysis reveals the cotton virome in the southern United States

Authors: ESCALANTE, CESAR - Auburn University; REYES, ANYI - Auburn University; Zhao, Chaoyang; Balkcom, Kipling; JACOBSON, ALANA - Auburn University; STRAYER-SCHERER, AMANDA - Auburn University; MARTIN, KATHLEEN - Auburn University; KOEBERNICK, JENNY - Auburn University; HUSETH, ANDERS - North Carolina State University; KOZIEL, EDMUND - Warsaw University Of Life Sciences; SMALL, IAN - University Of Florida; GREENE, JEREMY - Clemson University; OTULAK-KOZIEL, KATARZYNA - Warsaw University Of Life Sciences; MULVANEY, MICHAEL - Mississippi State University; PRICE, PAUL - Louisiana State University; ALCALÁ BRISEÑO, RICARDO - Oregon State University; BAG, SUDEEP - University Of Georgia; CONNER, KASSIE - Auburn University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2026
Publication Date: 2/23/2026
Citation: Escalante, C., Reyes, A.M., Zhao, C., Balkcom, K.S., Jacobson, A.L., Strayer-Scherer, A., Martin, K.M., Koebernick, J., Huseth, A., Koziel, E., Small, I., Greene, J., Otulak-Koziel, K., Mulvaney, M.J., Price, P.P., Alcalá Briseño, R.I., Bag, S., Conner, K. 2026. Metatranscriptomics analysis reveals the cotton virome in the southern United States. Scientific Reports. (2026). https://doi.org/10.1038/s41598-026-40828-5.
DOI: https://doi.org/10.1038/s41598-026-40828-5

Interpretive Summary: In recent decades, viral diseases have caused significant yield losses in the cotton industry. The cotton leafroll dwarf virus (CLRDV) is a newly emerging threat that has been identified in the U.S. cotton fields and is linked to various symptoms. However, these symptoms may not solely be caused by CLRDV; co-infection with other viruses could also be a contributing factor. To explore the presence of additional cotton viruses and investigate the potential for viral co-infections in the U.S. Cotton Belt region, ARS scientists in Auburn, AL collaborated with researchers from several universities. They collected cotton leaf samples from fields across the southern United States and analyzed their RNA components using high-throughput sequencing technology. The genetic analysis revealed the presence of CLRDV in all samples and identified 29 potential families of plant viruses co-infecting cotton. The information obtained in this study will help enhance our understanding of how co-infections involving CLRDV and other plant viruses might affect the physiology, product quality, and yield of cotton plants.

Technical Abstract: High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.