2008 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.
One area of specific interest within the group is functional regulatory sequences and networks. Transcription factors bind to specific DNA motifs and control the expression of genes. To computationally identify motifs we are evaluating CREAD (Comprehensive Regulatory Element Analysis Discovery) which was developed in Michael Zhang’s group at CSHL. The objective is directly related to NP 301 Component 2.
In the last 3 months we have continued to make use of the Ensembl infrastructure to store and visualize genomic data sets and are making use of the most recent release 49. We have continued to use and support the development of the plant ontology, including updates to the software, descriptions, and associations to terms. We have recently made available web services using the distributed annotations server that is native to Ensembl, and participated in the development and deployment of semantic services as part of the Virtual Plant Information Network (VPIN). More recent work in the lab has focused on the handling and interpretation of short sequence reads from the new sequencing technologies. The group has been evaluating methods for aligning data to reference genomes and using this information to identify single nucleotide variation.
The objective is directly related to NP 301 Component 3.
Hufford, K., Canaran, P., Ware, D., Mcmullen, M.D., Gaut, B. 2007. Tissue-specific expression of maize domestication and crop improvement loci. Plant Physiology. 144:1642-1653.
Lu, C., Jeong, D., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, D., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., Green, P. 2008. Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs). Proceedings of the National Academy of Sciences. 105(12):4951-4956.
Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., Miguel, P.S., Mullikin, J., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.L., Stein, L., Ware, D., Jackson, S., Soderlund, C., Wing, R. 2008. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza. Genome Research. 9:R45.1-R45.15.
Jaiswal, P., Avraham, S., Buckler Iv, E.S., Casstevens, T., Hebbard, C., Liang, C., Ni, J., Ravenscroft, D., Ren, L., Stein, L., Spooner, W., Tecle, I., Thomason, J., Wei Xuehong, Ware, D., Youens-Clark, K., Yap, I., Mccouch, S., Tung, C. 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36:D947-D953.
Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E., Mccouch, S., Pujar, A., Reiser, L., Rhee, S., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Zapata, F., Ware, D. 2008. The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research. 36:D449-D454.
Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., Mccouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Ware, D., Zapata, F. 2005. Plant ontology (po): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics. 6:388-397.
Ilic, K., Kellogg, E.A., Jaiswal, P., Zapata, F., Stevens, P.F., Vincent, L.P., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M., Whitman, N.T., Mccouch, S.R., Schaeffer, M.L., Ware, D., Stein, L.D., Rhee, S.Y. 2006. Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology 143:587-599
Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E.A., Mccouch, S.R., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L.D., Stevens, P.F., Vincent, L.P., Zapata, F., Ware, D. 2007. The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations. Nucleic Acids Research 36: Database issue D449-D454