# Metatranscriptomics analysis reveals the cotton virome in the southern United States

## TL;DR

This study used high-throughput sequencing to identify viruses infecting cotton plants in the southern US, finding a diverse virome including a common virus and several RNA and DNA virus families.

## Contribution

The study provides a comprehensive catalog of cotton-infecting viruses and highlights the prevalence of co-infections in cotton fields.

## Key findings

- Cotton leafroll dwarf virus genome was detected in all tested cotton samples.
- 29 putative virus families were identified, with seven RNA virus families being more prevalent.
- The findings may help understand how virus co-infections affect cotton plant health and yield.

## 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.

The online version contains supplementary material available at 10.1038/s41598-026-40828-5.