Metatranscriptomics analysis reveals the cotton virome in the southern United States
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.
Authors
- Kathleen Martin (ORCID: https://orcid.org/0000-0002-6654-2668)
- Kassie Conner (ORCID: https://orcid.org/0000-0001-5654-673X)
- Michael J. Mulvaney (ORCID: https://orcid.org/0000-0002-7947-1467)
- Kipling S. Balkcom (ORCID: https://orcid.org/0000-0003-0762-7386)
- Ian Small (ORCID: https://orcid.org/0000-0001-5300-1216)
- Edmund Kozieł (ORCID: https://orcid.org/0000-0001-6646-1254)
- Sudeep Bag (ORCID: https://orcid.org/0000-0003-3724-7341)
- Amanda Strayer-Scherer (ORCID: https://orcid.org/0000-0002-9073-8038)
- Jenny Koebernick (ORCID: https://orcid.org/0000-0002-9684-7147)
- Alana L. Jacobson (ORCID: https://orcid.org/0000-0002-1296-4654)
- Katarzyna Otulak-Kozieł (ORCID: https://orcid.org/0000-0001-9424-1662)
- Chaoyang Zhao (ORCID: https://orcid.org/0000-0003-3378-3163)
- Anders S. Huseth (ORCID: https://orcid.org/0000-0002-5273-8555)
- Paul P. Price (ORCID: https://orcid.org/0000-0002-1004-3616)
- Ricardo I. Alcalá Briseño
- Jeremy K. Greene
- Anyi M. Reyes
Institutions
- Pennsylvania State University (US)
- Louisiana State University Agricultural Center (US)
- North Carolina State University (US)
- University of Georgia (US)
- Warsaw University of Life Sciences (PL)
- Purdue University West Lafayette (US)
- National Soil Dynamics Research Laboratory (US)
- Auburn University System (US)
- Clemson University (US)
- Auburn University (US)
- Michigan State University (US)
- Quincy University (US)
- Mississippi State University (US)
Publication Details
- Journal
- Scientific Reports
- Published
- 2026-02-23
- DOI
- https://doi.org/10.1038/s41598-026-40828-5
- Primary Topic
- Plant Virus Research Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- U.S. Department of Agriculture
- Auburn University
- National Institute of Food and Agriculture
- Agricultural Research Service