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Associate Professor of Plant Biology
Department of Plant Biology Plant Biology Department |
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Research
My research activities are centered on genomic aspects of plant biology and plant pathogens. My research primarily involves projects focused on high throughput sequencing, functional genomics, comparative genomics, and bioinformatics.
Rice Genomics and Bioinformatics
Worldwide, rice is one of the world’s most important crop plants with 50% of the population dependent on rice as a food source. Furthermore, rice is a member of the grass family (Poaceae) and is considered a model species for the cereals as it has a near-complete finished genome and a wealth of resources for functional genomics studies. One important component of a genome sequence is accurate, uniform annotation of genes, gene models, and gene function. Using a suite of automated, semi-automated, and manual computational methods, my group has annotated the rice genome (http://rice.tigr.org). We have generated pseudomolecules to represent the 12 rice chromosomes, modeled genes, incorporated experimental evidence into gene models, generated deep, rich functional annotation of the genome, and identified related sequences in other plant species (Yuan et al. Plant Physiol. 2005; Ouyang et al. 2007). We have deployed a genome browser for the rice genome in which >60 tracks of annotation are displayed (http://www.tigr.org/tigr-scripts/osa1_web/gbrowse/rice/).
We have identified nearly 42,000 non-transposable element related genes in the rice genome and have initiated analyses of the rice genome and its predicted proteome to provide insights into the biology of this model species. The large number of genes in rice is attributable to the substantial segmental duplication that involved nearly half of the genome (Lin et al. 2006). One impact of this duplication is the generation of large gene families and in providing new genes for diversity. Indeed, nearly half of the predicted rice proteome can be found in paralogous families. We have analyzed alternative splicing in rice and observed that alternative splicing is not only widespread but also that a surprising number of alternative splice forms result in a significant change in coding sequence, suggesting a potential pathway for non-sense mediated decay of mRNAs in rice (Campbell et al. BMC Genomics 2006). Rice has an immense level of diversity that provides a genetic resource for improving germplasm. Using the Perlegen hybridization-based re-sequencing technology to identify single nucleotide polymorphism data, we are collaborating with multiple scientists to generate a “hapmap” for rice (http://oryzasnp.org; McNalley et al. Plant Physiol. 2006). With access to sequence data from 184 plant species, we have been able to examine the conservation of predicted rice genes throughout the Plant Kingdom (Zhu and Buell, Genome Research 2007). Through these analyses, we have been able to identify core sets of conserved genes across not just the Poaceae but also angiosperms and the Plant Kingdom.
Solanaceae Genomics and Bioinformatics
The Solanaceae family contains several species relevant to agriculture including potato, tomato, tobacco, petunia, and pepper. While selected for diverse morphological features such as fruit (tomato, pepper, eggplant), tubers (potato), leaves (tobacco), and flowers (petunia), the Solanaceae share a high extent of sequence similarity. Previous work in my group has focused on generation of genomic resources for potato (Ronning et al. Plant Physiol. 2003; Rensink et al. Genome 2005a), identifying disease resistance genes in wild potato species (Song et al. PNAS 2003), and expression profiling (Rensink et al. IFG 2005b). We have also initiated comparative genomic analyses within the Solanaceae (Rensink et al. BMC Genomics 2005) which confirmed earlier reports of conservation within the Solanaceae but also revealed a higher degree of species specific sequences within the Solanaceae than previously documented. My group is currently involved in the international Potato Genome Sequencing Consortium (http://www.tigr.org/tdb/sol/). In this project funded by the National Science Foundation, we are generating sequence from chromosome VI of potato. We are creating a suite of genomic and bioinformatic tools and resources for the potato community. This involves annotation of potato genome sequences and development of a “web portal” so that potato breeders and geneticists, along with other Solanaceae researchers, can access the genome sequence, annotation, and expression data in a meaningful, user-friendly manner.
Genomics and Bioinformatics of Plant Pathogens
My work on plant pathogens involves genome sequencing, comparative genomics, and bioinformatics. We have generated a plant pathogen genome sequence and annotation resource (http://cpgr.plantbiology.msu
Current Funding Support
An annotation resource for the rice genome; NSF; 01/01/04-6/30/08
Sequencing multiple and diverse rice varieties to allow connection of whole-genome variation with phenotype; USDA; 11/15/05-11/14/08
Whole Genome Sequencing of Pythium ultimum; USDA; 12/15/06-12/14/08
A comprehensive genome-based diagnostics resource and pipeline for identification of threatening plant pathogens; USDA; 3/1/06-2/28/09
Generation of potato sequence and annotation resources; NSF; 10/01/06-9/30/09
Workshop on cyberinfrastructure tools for genomics; NSF; 01/01/08 - 12/31/08
Comparative Genomics Resources for the Solanaceae: Tools and Resources for Cross-species Translational Genomics; USDA; 11/30/07-12/31/10
Select Publications
Lin, H., Ouyang, S., Egan, A., Nobuta, K., Haas, B.J., Zhu, W., Gu, X., Silva, J.C., Meyers, B.C., and Buell, C. R. 2008. Characterization of paralogous protein families in rice. BMC Plant Biology 8:18.
Haas, B.J., Salzberg, S., Zhu, W., Pertea, M., Allen, J., Orvis, J., White, O., Buell, C.R., and Wortman, J.R. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9(1):R7.
Van Deynze, A., Stoffel, K., Buell, C.R., Kozik, A., Liu, J., van der Knapp, E., and Francis, D. 2007. Diversity in conserved genes in tomato. BMC Genomics 8:465.
Campbell, M. A., Zhu, W., Jiang, N., Lin, H., Ouyang, S., Childs, K.L., Haas, B.J., Hamilton, J. P., and Buell, C. R. 2007. Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiology145:1311-1322.
Thibaud-Nissen, F., Campbell, M., Hamilton, J., Zhu, W., and Buell, C. R. 2007. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. BMC Genomics 8:388.
Stupar, R.M., Bhaskar, P. B., Yandell, B.S., Rensink, W. A., Hart, A. L., Ouyang, S., Veilleux, R. E., Busse, J. S., Erhardt, R. J., Buell, C. R., and Jiang, J. 2007. Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176:2055-2067.
Zhu, W., and Buell. C. R. 2007. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Research 17:299-310.
Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissan, F., Malek, R.L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J., and Buell, C. R. 2007. The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Research 35 (Database issue) :D883-D887; doi:10.1093/nar/gkl976.
Childs, K., Hamilton, J., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P. B., Town, C.D., Buell, C. R., and Chan, A.P. The TIGR Plant Transcript Assemblies Database. 2007. Nucleic Acids Research 35 (Database issue):D846-D851; doi:10.1093/nar/gkl78.
Campbell, M.A., Haas, B.J., Hamilton, J., Mount, S.M., and Buell, C. R. 2006. Comprehensive analysis of alternative splicing in the rice genome and comparative analyses with Arabidopsis. BMC Genomics 7:327.
Lin, H., Zhu, W., Silva, J., Gu, X., and Buell, C. R. 2006. Intron gain and loss in segmentally duplicated genes in rice. Genome Biology 7(5):R41.
Rensink, W.A., Lee, Y., Liu, J., Iobst, S., Ouyang, S., and Buell, C. R. 2005. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6:124.
Joardar, V., Lindeberg, M., Jackson, R., Selengut, J., Dodson, R. J., Brinkac, L.M., Daugherty, S.C., Deboy, R., Durkin, A. S., Giglio, M. G., Madupu, R., Nelson, W. C., Rosovitz, M.J., Sullivan, S., Haft, D. H., Creasy, T., Davidsen, T., Zafar, N., Zhou, L., Halpin, R., Holly, T., Khouri, H., Feldblyum, T. V., White, O., Fraser, C. M., Chatterjee, A. K., Cartinhour, S., Schneider, D., Mansfield, J., Collmer, A., and Buell, C. R. 2005. Whole genome sequence analysis of Pseudomonas syringae pv phaseolicola 1448A reveals sequence divergence among pathovars in genes involved in virulence, transposition, and unknown function. Journal of Bacteriology 187:6488-6498.
The International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436:793-800.
Rensink, W. A., Hart, A., Liu, J., Ouyang, S., Zismann, V., and Buell, C. R. 2005a. Analyzing the potato abiotic stress transcriptome using Expressed Sequence Tags. Genome 48:598-605.
Rensink, W. A., Iobst, S., Hart, A., Stegalkina, S., Liu, J., and Buell, C. R. 2005b. Gene expression profiling of potato responses to cold, heat, and salt stress. Integrative and Functional Genomics 5: 201-207.
Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., Wortman, J., and Buell, C.R. 2005. The TIGR Osa1 rice genome annotation database. Plant Physiology 138:18-26.
Joardar, V., Lindeberg, M., Collmer, A. and Buell, C. R. 2005. Lineage specific regions in Pseudomonas syringae pv tomato DC3000 are associated with features of lateral gene transfer. Molecular Plant Pathology 6: 53-64.
Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M, Jones, K. M., Henikoff, S., Buell, C. R., and Jiang, J. 2004. Sequencing of a rice centromere uncovers active genes. Nature Genetics 36:138-145.
Ouyang, S. and Buell, C. R. 2004. The TIGR Plant Repeat Databases: A Collective Resource for Identification of Repetitive Sequences in Plants. NAR 32 Database Issue: D360-363.
Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., Dodson, R. J., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Daugherty, S. Brinkac, L., Beanan, M. J., Haft, D. H., Nelson, W. C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Vanaken, S. E., Feldblyum, T. V., D'Ascenzo, M., Deng, W. L., Ramos, A. R., Alfano, J. R., Cartinhour, S., Chatterjee, A. K., Delaney, T. P., Lazarowitz, S. G., Martin, G. B., Schneider, D. J., Tang, X., Bender, C. L., White , O., Fraser, C. M., and Collmer, A. 2003. The complete sequence of the tomato and Arabidopsis pathogen, Pseudomonas syringae pv tomato DC3000. Proc. Natl. Acad. Sci. USA 100:10181-10186.
Song, J., Bradeen, J. M., Naess, S. K., Raasch, J. A., Wielgus, S. M., Haberlach, G. T., Liu, J., Kuang, H., Austin-Phillips, S., Buell, C. R., Helgeson, J. P., and Jiang, J. 2003. Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight pathogen. Proc. Natl. Acad. Sci. USA 100:9128-9133.
Ronning, C. M., Stegalkina, S., Ascenzi, R., Bougri, O., Hart, A., Utterback, T., Vanaken, S., Reidmuller, S., White, J., Cho, J., Karamycheva, S., Pertea, G. M., Lee, Y., Karamycheva, S., Sultana, R., Tsai, J., Quackenbush, J., Griffiths, H. M., Restrepo, S., Smart, C. D., Fry, W. E., van der Hoeven, R., Tanksley, S., Zhang, P., Jin, H., Yamamoto, M., Baker, B. J., and Buell, C. R. 2003. Comparative analyses of potato Expressed Sequence Tag libraries. Plant Physiology 131: 419-429.
People in the Buell Laboratory
Kevin Childs, Bioinformatician/Research Associate
Michael Geoffroy, Research Assistant
John Hamilton, Bioinformatician
Haining Lin, Bioinformatician
Steven Lundback, Research Assistant
Brett Whitty, Bioinformatician
Brieanne Vaillancourt, Lab Assistant
