2012 Annual Report
1. Enhance our knowledge of plant genome structure, organization and evolution through computational and experimental approaches. 2. Develop and implement standards for plant genome databases. This includes development of vocabulary, methods, database structures and visualization software to facilitate data integration and interoperability.
Aim 2: We expanded existing efforts to characterize gene networks, targeting networks in root and floral architecture and response to abiotic stress. The miRNA- arabidopsis gene root network efforts were extended through the addition of promoter screens and the incorporation of Y2H data. In maize ~15 high-confidence candidate genes were identified as determinacy factors of developmental networks controlling inflorescence architecture, through differential mutant profiles. We refined previous workflows for core promoter motifs and applied this to 8 eukaryote genomes and have begun work to characterize cis regulatory motifs (CRMs) combinations in co-expression networks. Using three maize inbred Zea mays lines that showed different tolerance to waterlogging, 5 miRNAs families were identified and are likely key regulators under short-term waterlogging and participate in signal transduction at the early stage of hypoxia conditions. Our previous work in sorghum reported in last year’s report was published this year.
Aim 3: This aim actively contributes to the scientific leadership, development, and community outreach for three collaborative infrastructure projects: Gramene/Ensembl (NSF, EBI), iPlant (NSF), and Systems Biology Knowledge Base (DOE) and contributes US-EC taskforce on Plant Biotechnology. The iPlant collaborative provides an infrastructure for hosting data; access to high performance computes from the command line or a graphical user interface called the Discovery Environment (DE); virtual hosting (Atmosphere) similar to the Amazon cloud; and community standards. More recent work has focused on evaluating de novo assembly tools to support plant genome assembly, expression profiling and genotyping services, and the development of the Taxon Name Resolution Service (TRNS). The KBase project award was made in summer 2011. The project is developing infrastructure to support modeling development for plants, microbes and meta-communities with a focus on DOE objectives.
This work was done in collaboration with USDA ARS scientists at several locations, as well as public- and private-sector scientists at Cold Spring Harbor Laboratory, Texas A&M, UC Davis, European Bioinformatics Institute and and Pioneer/Dupont.
This work was done in collaboration with scientist at National Key Lab. of Crop Genetic Improvement Huazhong Agricultural University, Wuhan.
Ware, D., Thannhauser, T.W., White, R.A., Giovannoni, J.J. 2012. The tomato genome sequence provides insight into fleshy fruit evolution. Nature. 485:635-641. DOI: 10.1038/nature11119.
Liu, Z., Kumari, S., Zhang, L., Zheng, Y., Ware, D. 2012. Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLoS One. 7(6):e39786.
Dugas, D.V., Monaco, M.K., Olsen, A., Klein, R.R., Kumari, S., Ware, D., Klein, P.E. 2011. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. Biomed Central (BMC) Genomics. 12:Article 514.
Matija, D., Ruxandra Carvunis, A., Charloteaux, B., Galli, M., Pevzner, S.J., Tasan, M., Stein, J., Spooner, W., Ware, D., Braun, P., Ecker, J.R., Hill, D.E., Roth, F.P., Vidal, M. 2011. Evidence for network evolution in an arabidopsis interactome map. Science. 333(6042):601-607.