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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #315537
Title: Small RNA deep sequencing revealed that mixed infection of known and unknown viruses were common in field collected vegetable samples

Author
item Padmanabhan, Chellappan
item ZHENG, YI - Boyce Thompson Institute
item Li, Rugang
item FEI, ZHANGJUN - Boyce Thompson Institute
item Ling, Kai-Shu

Submitted to: American Phytopathological Society Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 5/8/2015
Publication Date: 8/1/2015
Citation: Padmanabhan, C., Zheng, Y., Li, R., Fei, Z., Ling, K. 2015. Small RNA deep sequencing revealed that mixed infection of known and unknown viruses were common in field collected vegetable samples. American Phytopathological Society Abstracts. P. 516.

Interpretive Summary:

Technical Abstract: In an effort to characterize the causal agents for plant diseases in field collected samples using the small RNA deep sequencing technology, numerous known or novel viruses and viroids were identified. In many cases, a mixed infection with multiple pathogen species was common. Such situation complicated the accurate disease diagnosis and determination of the actual causal agent for the disease. With mixed infection of multiple viruses, the traditional concept of disease diagnosis based on specific virus detection may need to be fundamentally changed. Therefore, proper strategies could be deployed for effective disease management based on the actual involvement of multiple viruses on the crop. Using nearly 200 sRNA libraries prepared from various vegetable samples collected from around the world, and a bioinformatics pipeline developed specifically for virus identification with deep sRNA sequencing datasets, many viruses and viroids were tentatively identified. Their characterization for validation and complete genome sequences were carried out through gap filling and 5’ RACE analysis. The preliminary analysis and the advantage of small RNA sequencing for virus identification will be presented.