2011 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.
To support the baseline annotation objectives, gene trees were generated for 10 plant genomes as well as 4 model species (human, drosophilia, c. elegans, and yeast). The gene trees serve as a foundation for comparative maps between species and evolutionary analyses within species. This framework has provided the foundation for projection of functions for similar genes in different plant species). Whole genome alignments between a reference dicot (Arabidopsis) and monocot (rice) serve as an additional support that complements protein based comparisons. Primary structural and functional annotations were generated for the updated RefGenV2 assembly of maize. More recent work has focused on evaluating de novo assembly tools to support plant genome assembly from next generation sequencing reads. This work is part of the NSF Gramene project, and the USDA/ DOE/NSF Maize Sequencing project.
The developed primary annotations have contributed to understanding natural variation and genome stability- specifically how genes are maintained and lost, and to generate the current patterns of maize variation. In the last year, we also studied within species variation in grape and maize. Maize variation data was generated from 100 inbred lines. 55 million high confidence DNA sequence variations were identified. This work was done in collaboration with the NSF sponsored Gramene and Maize Diversity projects, EBI Ensembl genomes, and USDA ARS researchers.
Resources were also developed to support the identification of the promoter sequences where transcription factors bind to regulate gene expression and to identify regulatory networks associated with plant development and response to abiotic stresses. Using computational methods, known core promoter motifs were globally evaluated from eukaryotes and then characterized in 6 plant genomes. Predicted binding sites for more than 90 promoters have been identified across the 6 plant genomes. Also, the prediction of gene targets for regulation by maize microRNA's was carried out.
Schnable, P., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Wing, R., Wilson, R., Zhang, L., Chia, J., Narechania, A. 2009. The B73maize genome: complexity, diversity, dynamics. Science. 326(5956):1112-1115.
Liang, C., Mao, L., Ware, D., Stein, L. 2009. Evidence-based gene predictions in plant genomes. Genome Research. 10(2):1912-1923.
Brook, Iii, L., Strable, J., Ware, D., Nettleton, D., Scanlon, M.J. 2009. Microdissection of Shoot Meristem Functional Domains. PLoS Genetics. 5(5): e1000476. DOI: 10.1371/journal.pgen.1000476.
Youens-Clark, K., Faga, B., Stein, L., Ware, D. 2009. CMap 1.01: a comparative mapping application for the internet. Bioinformatics. 25(22):3040-3042.
Zhou, S., Fusheng, W., Pasternak, S., Ware, D., Wing, R., Livny, M., Schwartz, D.C. 2009. A single molecule scaffold for the maize genome. PLoS Genetics. 5(11):1-14.
Paterson, A.H., Bowers, J.E., Maher, C.A., Narechania, A., Zhang, L., Ware, D., Messing, J., Rokhsar, D.S. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457:551-556.
Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., Springer, N.M. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research. 20(12):1689-1699.
Wicker, T., Narechania, A., Sabot, F., Stein, J., Giang, V., Graner, A., Ware, D., Stein, N. 2008. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. Biomed Central (BMC) Genomics. 9:518.
Eveland, A.L., Nagasawa, N., Goldshmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D., Jackson, D. 2010. Digital gene expression signatures for maize development. Plant Physiology. 154(3):1024-1039.
Brady, S.M., Zhang, L., Megraw, M., Martinez, N.J., Jiang, E., Yi, C.S., Ware, D., Walhout, A.J., Benfey, P.N. 2011. A stele-enriched gene regulatory network in the arabidopsis root. EMBO Journal. 7:459.
Zhang, L., Chia, J., Kumari, S., Stein, J.C., Liu, Z., Narechania, A., Maher, C.A., Guill, K., Mcmullen, M.D., Ware, D. 2009. Genome-wide characterization of maize miRNA genes. PLoS Genetics. 5(11): e1000716. DOI: 10.1371/journal.pgen.1000716.
Bastow, R., Beynon, J., Estelle, M., Friesner, J., Grotewold, E., Lavagi, I., Lindsey, K., Meyers, B., Provart, N., Benfey, P., Birney, E., Braun, P., Brendel, V., Buell, R., Caccamo, M., Carrington, J., Cherry, M., Ecker, J., Eppig, J., Forster, M., Gutierrez, R., Hilson, P., Huala, E., Katari, M., Kersey, P., Kudla, J., Ma, H., Matsui, M., Matthews, K., May, S., Mayer, K., Millar, A., Millar, H., Mjolsness, E., Mockler, T., Nikolau, B., Nordborg, M., Rawlings, C., Schofield, P., Schoof, H., Schroeder, J., Sen, T.Z., Stanzione, D., Town, C., Toyoda, T., Vision, T., Walsh, S., Wang, X., Ware, D., Weckwerth, W., Yang, W. 2010. An international bioinformatics infrastructure to underpin the Arabidopsis community. The Plant Cell. 22(8):2530-2536.