2013 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.
While the genomes provide the parts list, our work on gene networks supports the characterization of gene involved in development and response to stress. We have extended the Arabidopsis miRNA gene root network by identify potential upstream regulators for an additional 57 genes and are developing genetic resources to validate these networks in plants. In maize we have characterized grass specific gene networks associated with flower development and architecture using expression and DNA binding profiles of maize flower development mutants. We continue to refine workflows for to understand the architecture of the sequence involved in when and where a gene is expressed (core promoter motifs) and applied this to 8 eukaryote genomes.
Recent technological advancements have led to an expansion of data in the biological sciences. Managing, accessing, integration and interpretation of the data is now one of the major challenges in agriculture science. In the past year, this project has contributed to the scientific leadership, development, and community outreach for three collaborative infrastructure projects which support open data and service initiatives for agriculture: Gramene/Ensembl (NSF, EBI), iPlant (NSF), and Systems Biology Knowledge Base (DOE). In the last year progress has been made on infrastructure for hosting data and access to high performance computes from the command line or a graphical user interface (Web). The resources have focused on high priority targets which support data integration, genome annotation, phenotype association and network analyses. In the last year we have organized or participated in more than 10 meetings to support training, vision and standards for the agricultural and broader life science community.
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, Oregon State University, European Bioinformatics Institute, DOE National laboratories, and Pioneer/DuPont.
Monaco, M.K., Sen, T.Z., Dharmawardhana, P., Ren, L., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P., Naithani, S., Cannon, E. 2013. Maize metabolic network construction and transcriptome analysis. The Plant Genome. 6(1):DOI:10.3835/plantgenome2012.09.0025.
Spooner, W., Youens-Clark, K., Staines, D., Ware, D. 2012. GrameneMart: the biomart data portal for the gramene project. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar056.
Regulski, M., Lu, Z., Kendall, J., Donoghue, M.T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., Mccombie, R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R.A. 2013. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. DOI: 10.1101/gr.153510.112.