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Title: Understanding the global distribution of tomato viruses and viroids using next-generation sequencing technology

item Ling, Kai-Shu
item Li, Rugang
item GAO, SHAN - Boyce Thompson Institute
item FEI, ZHANGJUN - Boyce Thompson Institute

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/22/2013
Publication Date: 6/24/2013
Citation: Ling, K., Li, R., Gao, S., Fei, Z. 2013. Understanding the global distribution of tomato viruses and viroids using next-generation sequencing technology. The 4th International Symposium on Tomato Diseases and 28th U.S. Annual Tomato Disease Workshop. p 24.

Interpretive Summary: N/A

Technical Abstract: Tomato (Solanum lycopersicum L.) originated in the Americas and is one of the most widely grown vegetables in the world. The modern transportation system, the increasing global seed trade, and the off-shore hybrid seed production have created greater opportunities for potential broader geographic distribution of viruses and other pathogens in tomato and other crops. Although general virus detection tools [such as enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR)] for a number of tomato viruses are very useful, for the new or emerging viruses and viroids, such detection methods may not be available. Since there are more than 100 viruses infecting tomato plants, choosing which viruses to be tested is a challenging task. For new or emerging viruses without a priori knowledge, an effective management relies on timely identification and characterization of the causal agent(s) for the disease. In recent years, next-generation sequencing technologies have been applied to plant virus identification. One of the promising technologies is the deep sequencing and assembly of virus-derived small RNAs (sRNAs). In collaboration with seed companies, a new research project was initiated in 2012 to conduct a global survey of tomato viruses and viroids using deep sequencing of sRNAs. Several hundreds of samples have been collected in several major tomato seed producing countries around the world and nearly 100 sRNA libraries were generated and sequenced with the Illumina HiSeq system. We developed a bioinformatics pipeline for efficient identification of known and novel viruses and viroids, based on alignment and assembly of sRNA sequences. It is anticipated that a comprehensive tomato virus and viroid inventory will be developed and a general global virus distribution map will be generated. The success of this project will lead us to determine reasonable phytosanitary requirements, to conduct proper risk assessment, and to recommend suitable disease management strategies.