Location: Vegetable Research2013 Annual Report
1a. Objectives (from AD-416):
Specific objectives are to 1) Develop a global tomato virome and virus distribution map through extensive virus survey and next generation sequencing of small RNAs. 2) Develop tomato translational genomic tools through transcriptome analysis to identify genes that are associated with virus resistance.
1b. Approach (from AD-416):
Dr. Fei’s lab recently received a National Science Foundation (NSF) grant (2011-2013) entitled “BREAD: Determining the Pan-African crop virome: understanding virus diversity, distribution and evolution and their impacts on crop production in Africa” and the bioinformatics tools developed under that grant will have a direct application to the current project. Fei’s group has also developed a Tomato Functional Genomics Database, which includes a set of interfaces and tools that allow users to mine, analyze, and integrate large-scale tomato gene expression, metabolite profile, and small RNA datasets. A web-based package, Plant MetGenMAP, which can identify significantly changed pathways and biological processes based on user-given gene expression and/or metabolite profile datasets, was also developed. Fei’s group developed a de novo transcriptome assembly package, iAssembler, which can assemble ESTs generated using Sanger and/or 454 pyrosequencing technologies with much higher accuracy. Together with Dr. Giovannoni’s group, Fei’s group developed a high-throughput strand-specific Illumina RNA-Seq library preparation protocol and a small RNA library preparation protocol, which can be directly used for the current project. Dr. Fei’s group has been extensively involved in analyzing tomato genome sequences. The number of proteins with typical R-gene domains in tomato, potato, Arabidopsis, grape and rice genomes have been identified, which will serve as a backbone of R-gene candidates to be used in the current project. Specifically, Dr. Fei will serve as a contact person in performing small RNA deep sequencing and RNA-seq using an Illumina HiSeq 2000 system at the Cornell University core sequencing facility, provide bioinformatics support in sequence analysis and virus and viroid identification, assist in generating a global tomato virus distribution map, and identify SNPs and candidate R-genes, and molecular marker development.
3. Progress Report:
Research in this subordinate project relates to inhouse project Objective 1: Develop sensitive diagnostic tools for the emerging viral diseases of greenhouse tomatoes and bacterial diseases on vegetable Brassicas. Tomato (Solanum lycopersicum L.), originated in South America, and it 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 broader geographic distribution of viruses and other pathogens in tomato and other crops. Although, general virus detection tools (including serological and molecular) 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, effective management relies on timely identification and characterization of the causal agent(s) of a disease. In recent years, next-generation sequencing technologies have been applied for plant virus identification. One of the promising technologies is the deep sequencing and assembly of virus-derived small RNAs (sRNAs). A global survey of tomato viruses and viroids using deep sequencing of sRNAs was initiated in 2012. Hundreds of samples have been collected in several major tomato seed producing countries around the world and a total of around 100 small RNA libraries have been sequenced at Weill Cornell Medical College. The sRNA sequences have been processed and analyzed for efficient identification of virus sequences using a bioinformatics pipeline. 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.