Virome Profiling via sRNA-Seq and Sample-Level Coding-Region Diversity of Tomato Brown Rugose Fruit Virus in Protected Tomato Crops in Xinjiang.
- 1Institute of Plant Protection, Xinjiang Uygur Autonomous Region Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Xinjiang Key Laboratory of Agricultural Bio-Safety, Urumqi 830091, China.
- 2College of Agronomy, Xinjiang Agricultural University, Urumqi 830091, China.
Abstract
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.
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BibTeX
@article{li2026virome,
title = {{Virome Profiling via sRNA-Seq and Sample-Level Coding-Region Diversity of Tomato Brown Rugose Fruit Virus in Protected Tomato Crops in Xinjiang.}},
author = {Jiecai Li and Xin Huang and Wenfang Luo and Junhui Zhou and Xiang Zhang and Siqiong Tang and Wei He and Jianjun Xu},
journal = {Viruses},
year = {2026},
month = oct,
doi = {10.3390/v18101127},
url = {https://europepmc.org/article/MED/42944047},
note = {CC BY},
}
RIS
TY - JOUR
TI - Virome Profiling via sRNA-Seq and Sample-Level Coding-Region Diversity of Tomato Brown Rugose Fruit Virus in Protected Tomato Crops in Xinjiang.
AU - Jiecai Li
AU - Xin Huang
AU - Wenfang Luo
AU - Junhui Zhou
AU - Xiang Zhang
AU - Siqiong Tang
AU - Wei He
AU - Jianjun Xu
PY - 2026
DA - 2026/10/11
JO - Viruses
DO - 10.3390/v18101127
UR - https://europepmc.org/article/MED/42944047
AB - 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.
SN - 1999-4915
ER -