Virome Profiling via sRNA-Seq and Sample-Level Coding-Region Diversity of Tomato Brown Rugose Fruit Virus in Protected Tomato Crops in Xinjiang

Viral diseases threaten protected tomato production in Xinjiang, China, yet the virus spectrum in symptomatic crops and the local sequence context of Tomato brown rugose fruit virus (ToBRFV) remain incompletely characterized. We used pooled small-RNA sequencing for virus discovery and individual reverse transcription PCR (RT-PCR)/Sanger confirmation in 116 symptomatic tomato samples and compared nine Xinjiang ToBRFV coding-region genomes with 435 curated public GenBank sequences. Nine viruses were identified in the symptomatic tomato samples, with ToBRFV being the most frequently detected (113/116, 97.4%). Virus co-detections occurred in 115 samples (99.1%), with four-virus combinations being the most common. In the 444-sequence ToBRFV coding-region dataset, the nine Xinjiang genomes obtained in this study represented distinct exact coding-sequence types and occupied multiple phylogenetic placements; 139 biallelic segregating sites were observed among them. These results document complex multi-virus co-detection in symptomatic protected-tomato samples and provide a local ToBRFV sequence resource. Because sampling was symptom-targeted and the genome set was small, representative sampling and epidemiological metadata are required to estimate regional prevalence, ToBRFV diversity and transmission history.