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.