Associate Professor of Plant Biology
Ph.D., 1992, Utah State University, Logan, UT
Department of Plant Biology
Michigan State University
East Lansing, MI 48824-1312 USA
Phone: (517) 353-5597
Fax: (517) 353-1926
e-mail:buell@msu.edu
http://buell-lab.plantbiology.msu.edu
Plant Biology Department
College of Natural Science
Michigan Agricultural Experiment Station
Genetics Graduate Program
Quantitative Biology Initiative
Plant Breeding, Genetics, & Biotechnology Program
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.plantbiology.msu.edu/). 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://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/).
back to the top
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 (McNalley et al. Plant Physiol. 2006), we are collaborating with multiple scientists to generate a “hapmap” for rice (http://oryzasnp.plantbiology.msu.edu/). 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.
back to the top
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://solanaceae.plantbiology.msu.edu/). 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.
back to the top
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.edu), termed the Comprehensive Phytopathogen Genome Resource (CPGR), which is populated with all plant pathogen genome sequence data including viruses, bacteria, fungi, stramenopiles, and nematodes and provides genome/annotation data-mining and visualization tools. In this collaborative project (Jan Leach (Colorado State University), Ned Tisserat (Colorado State University), Tom Powers (University of Nebraska) and Andre Levesque (Agriculture and Agri-Food Canada)), we are developing diagnostic markers for three pathogens using genomics-based methods. These three “proof-of-concept” sub-projects will allow for the development and deployment of genomic and bioinformatic tools that will enable the broader plant pathology community, including diagnosticians and extension agents, to employ genomics in diagnostics.
We are also currently sequencing two strains of the ubiquitous plant pathogen, Pythium ultimum, and will be performing a comparative genomics analysis between the two isolates and with other oomycetes (http://pythium.plantbiology.msu.edu/).
back to the top
Project Web Sites
Rice Genome Annotation
OryzaSNP Database
Pythium Genome Database
Comprehensive Pythopathogen Genome Resource
SolCAP
Solanaceae Genomics Resource
Biofuel Feedstock Genomics Resource
MSU Plant Repeats Database
Buell Lab Website
back to the top
Current Funding Support
An annotation resource for the rice genome; NSF; 9/27/07-8/31/10
Whole Genome Sequencing of Pythium ultimum; USDA; 1/15/08-4/14/10
A comprehensive genome-based diagnostics resource and pipeline for identification of threatening plant pathogens; USDA; 10/01/07-2/28/10
Generation of potato sequence and annotation resources; NSF; 9/28/07-9/30/10
Comparative genomics resources for the Solanaceae: Tools and resources for cross-species translational genomics; USDA; 11/30/07-12/31/10
Computational Resources for Biofuel Feedstock Species; DOE & USDA; 8/15/08-8/14/11
Biochemical Pathway Mapping of Genes within Biofuel Feedstock Species; Michigan Agricultural Experiment Station;7/18/08-6/30/10
SolCAP: Translating Solanaceae sequence diversity and trait variation into applied outcomes through integrative research, education, and extension; USDA; 10/01/08-9/20/12
High throughput sequencing for comparative genomics of the Solanaceae; MSU Foundation; 7/1/08-6/30/12
Select Publications
McNally, K.L, Childs, K.L., Bohnert, R., Davidson, R.M., Zhao, K., Ulat, V.J., Zeller, G., Clark, R.M., Hoen, D.R., Bureau, T.E., Stokowski, R., Ballinger, D.J., Frazer, K. A., Cox, D.R., Padhukasahasram, B., Bustamante, C., Weigel, D., Mackill, D.J., Bruskiewich, R.M., Rätsch, G., Buell, C. R., Leung, H., and Leach, J. E. 2009. Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. PNAS, in press.
Thibaud-Nissen, F. Shu Ouyang, S., and Buell, C. R. 2009. Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics, in press.
Buell, C. R. 2009. Poaceae Genomes: Going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiology 149:111-116.
Kuang, H., Padmanabhan, C., Li, F., Kamei, A., Bhaskar, P., Ouyang, S., Jiang, J., Buell, C. R., and Baker, B. 2009. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Research 19:42-56.
Cheung, F., Win, J., Lang, J., Hamilton, J., Vuong, H., Leach, J. E., Kamoun, S., Lévesque, C. A., Tisserat, N., and Buell, C.R. 2008. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 9:542.
Jung, K., Dardick, C., Bartley, L. E., Cao, P., Phetsom, J., Canlas, P., Seo, Y. S., Shultz, M., Ouyang, S., Yuan, Q., Frank, B. C., Ly, E., Zheng, L., Jia, Y., Hsia, A. –P., An, K., Chou, H. H., Rocke, D., Lee, G. C., Schnable, P. S., An, G., Buell, C. R., and Ronald, P. C. 2008. Refinement of light-responsive gene lists using rice oligonucleotide arrays: Evaluation of gene-redundancy. PLoS One 3:e3337.
Iovene, M., Wielgus, S. M. Simon, P. W., Buell, C. R. and Jiang, J. 2008. Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 180:1307-1317.
Zhu, W., Ouyang, S., Iovene, M., O’Brien, K., Vuong, H., Jiang, J, and Buell, C. R. 2008. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics 9:286.
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.
Vencato, M., Tian, F., Alfano, J. R., Buell, C. R., Cartinhour, S., DeClerck, G. A., Guttman, D. S., Stavrinides, J., Joardar, V., Lindeberg, M., Bronstein, P. A., Mansfield, J. W., Myers, C. R., Collmer, A. and Schneider, D. J. 2006. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. Molecular Plant Microbe Interactions 19:1193-1206.
Cairney, J., Zheng, L., Cowels, A., Hsiao, J., Zismann, V., Liu, J., Ouyang, S., Thibaud-Nissen, F., Hamilton, J., Childs, K., Pullman, G. S., Zhang, Y., Oh, T., and Buell, C. R. 2006. Expressed Sequence Tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. Plant Molecular Biology 62:485-501.
Yan, H., Ito, H., Nobuta, K., Ouyang, S., Jin, W., Tian, S., Lu, C., Venu, R.C., Wang, G., Green, P.J., Wing, R.A., Buell, C.R., Meyers, B.C., and Jiang, J. 2006. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123-33.
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.
Avila-Adame, C., Gómez-Alpizar, L., Zismann, V., Jones, K. M., Buell, C. R., and Ristaino, J. B. 2006. Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Current Genetics 49:39-46.
Yan, H., Jin, W., Nagaki, K., Tian, S., Ouyang, S., Buell, C. R., Talbert, P. B., Henikoff, S., and Jiang, J. 2005. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17:3227-3238.
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.
The Rice Chromosomes 11 and 12 Sequencing Consortia. 2005. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology 3:20 doi:10.1186/1741-7007-3-20.
Kuang H., Marano, M. R., Wei, F., Wirtz, U., Wang, X., Liu, J., Shum, W. P., Zaborsky, J., Tallon, L. J., Rensink, W., Iobst S., Zhang, P., Tornqvist, C. E., Tek, A., Bamberg, J., Helegson, J., Fry, W., Luo, M.-C., Malcuit, I., Jiang, J., Buell, C. R., and Baker, B. 2005. The R1 resistance cluster contains three groups of independently evolving, Type I R1 homologues and shows substantial structural variation between haplotypes of Solanum demissum. Plant Journal 44:37-51.
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.
Gardiner, J. M., Buell, C. R., Elumalai, R., Galbraith, D.W., Henderson, D.A., Iniguez, A.L., Kaeppler, S.M., Kim, J.J., Liu, J., Zheng, L., and Chandler, V.L. 2005. Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica 50: 425-435.
The Rice Chromosome 3 Sequencing Consortium (C. R. Buell is corresponding contributor). 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research 15:1284-1291.
Restrepo, S., Meyers, K.L., del Poz, O., Martin, G.B., Hart, A., Buell, C.R., Fry, W.E., and Smart, C. D. 2005. Gene profiling of a compatible interaction between Phytophthora infestans and Solanum tuberosum suggests a role for carbonic anhydrase. Molecular Plant Microbe Interactions 18:913-922.
Rensink, W. A., Hart, A., Liu, J., Ouyang, S., Zismann, V., and Buell, C. R. 2005. 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. 2005. 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., Neumann, P., Zhang, D., Ouyang, S., Buell, C. R., Cheng, Z., and Jiang, J. 2005. Structure, divergence, and distribution of the CRR centromeric retrotransposon family in the rice genome. Molecular Biology and Evolution 22:845-855.
Sorghum Genomics Planning Workshop Participants. 2005. Toward sequencing the sorghum genome: a US National Science Foundation-sponsored workshop report. Plant Physiology 138:1898-1902.
Rensink, W.A. and Buell, C. R. 2005. Microarray expression profiling resources for plant genomics. Trends in Plant Science 10:603-609.
back to the top
