MSU Plant Biology Department

C. Robin Buell

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/). Working with researchers at the National Institute of Agrobiological Sciences (Tsukuba, Japan) and D. Schwartz (University of Wisconsin), we recently incorporated next generation sequencing (NGS) data from the reference accession (Nipponbare) as well data from the optical map to correct sequencing errors and misassemblies in the underlying IRGSP sequence. Using these refined reference pseudomolecules, we have revised our annotation to include new transcript and protein evidence, orthologous groups, community annotation, and new data-mining tools. Release of version 7 of our annotation is now available at http://rice.plantbiology.msu.edu/.
 
     As with other genomes, a large percentage of genes in the rice genome have no known function, remaining an enigma even eight years after completion of the rice genome. While correlative in nature, transcriptome expression patterns are informative with respect to deducing function as they can reveal associations with a biological process. Using publicly available rice gene expression data, we have performed gene correlation analyses to identify sets of genes that are functionally co-regulated. Using the WGCNA correlation network analysis protocol, we have identified modules of highly inter-connected genes within larger networks (Childs et al. 2011).  Examination of these modules reveals that these sets of genes have functional annotations that are consistent with the tissues/treatments in which they are expressed.  From fifteen expression datasets, we have identified 87 gene modules involving a total of 14,521 unique genes.  A total of 3,547 genes assigned to gene modules had no prior functional annotation (20% of all rice genes with no known function), and these genes can now be annotated as being members of defined gene modules.
 
      The Poaceae inhabit a wide range of environmental niches and possess a number of unique morphological, physiological, and developmental processes of agricultural relevance including floral/fruit development, drought tolerance, and C4  photosynthesis. This divergence occurred in the last 55-70 million years and it is intriguing how these traits evolved. In collaboration with Dr. Ning Jiang (MSU Horticulture Department), we used genomic sequences from 184 plant species to identify 861 rice genes termed “Conserved Poaceae Specific Genes” (CPSGs) that are conserved within the Poaceae family yet lack significant sequence similarity to non-Poaceae species.As measured through several gene metrics, the CPSGs are distinct from evolutionary conserved genes and transposable elements and the majority of CPSGs encode proteins with no known function (Campbell et al. 2007). We are using a two pronged approach to define the function of the CPSGs. First, we have performed expression profiling using a floral and seed developmental series from four Poaceae species (rice, maize, sorghum, and Brachypodium distachon) to identify orthologous genes expressed in parallel reproductive tissues in all four species (Davidson et al. 2011, 2012). Second, we are determining the function of a subset of our co-expressed orthologous CPSGs using mutant, knockout, knockdown, and/or over-expression studies in rice followed by phenotyping using a standardized set of metrics for floral/seed development and yield. 
 
         One intriguing feature of plant genomes is the high density of transposable elements, the so-called “jumping genes” initially discovered by Barbara McClintock in the 1940’s. One class of transposable elements, the Pack-MULEs, has the potential to create new genes in a genome.  In collaboration with Dr. Ning Jiang, MSU Horticulture Department, we are determining the potential for Pack-MULEs to create new genes in the rice genome through their transposition activity. This involves sequencing additional rice cultivars and exploring epigenetic and expression features of Pack-MULEs that indicate they may function as bona fide genes.   
 
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Potato Genomics and Bioinformatics
Potato is grown for its tuber, a below-ground storage organ that is not only calorie rich but also high in vitamins. Potato is the third most important crop on a worldwide basis and is the most significant non-grain crop species. More importantly, potato acreage in developing countries is increasing due to its wide adaptability, yield, and nutrition. My group was instrumental in generation of the potato genome sequence released in 2011 (Potato Genome Sequencing Consortium, 2011). In addition, we analyzed the potato transcriptome throughout development, abiotic stress, biotic stress and hormone treatment (Massa et al. 2011). Using the potato genome sequence, along with transcriptome sequences from cultivated potato accessions, we identified  single nucleotide polymorphisms (SNPs) in cultivated potato (Hamilton et al. 2011) and developed a 8303 SNP array to genotype cultivated potato (Felcher et al. 2012) and implement genomics-guided breeding approaches for potato. We recently completed an analysis of diversity in cultivated potato in which we were able to assess historic potato breeding efforts in the last 150 years and the differentiation of market classes (chip processing, frozen French fry processing, yellow fleshed, pigmented, etc) through targeted breeding efforts.
 
      Cultivated potato is a vegetatively propagated autotetraploid with a highly heterozygous genome, unique among other major crop and model plant species. With funding from the National Science Foundation, we are examining the role of heterozygosity, copy number variation, presence/absence variation, epigenetic features, and allele specific expression in vigor in potato. This project, in collaboration with scientists at MSU, Virginia Tech, and University of Wisconsin, will provide information on genomic features in a polyploidy that correspond with agronomic phenotypes. 
 
 
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Biofuel Feedstock Genomics
 
One source of renewable energy is the conversion of plant-based biomass (or feedstocks) into biofuels such as ethanol. A number of biofuel feedstock research programs are focused on improving biomass production in grass species such as maize (corn) and switchgrass. This is due to the potential for energy conversion of plant-derived biomass, established agricultural production methods for maize and switchgrass, and high biomass yields. My group has developed the Biofuel Feedstock Genomics Resource which provides a web-based portal or “clearing house” for genome sequence and annotation data, germplasm data, and large-scale functional genomic datasets for plant species relevant to biofuel feedstock production.
 
          In collaboration with Drs. Shawn Kaeppler, Natalia de Leon, and Mike Casler at the University of Wisconsin as part of the Great Lakes Bioenergy Research Center (http://glbrc.org), a research collaboration between MSU and University of Wisconsin, we are identifying natural variants in maize and switchgrass to target for improved biomass production and recalcitrance in these two species. Our work to date has included development of a maize gene atlas (Sekhorn et al. 2010), characterization of genotypic diversity in maize (Hansey et al. 2012), analysis of switchgrass transcriptome diversity, and development of an exon capture array for switchgrass. On-going efforts are focused on genotyping thousands of maize and switchgrass accessions for use in association mapping. These collaborative efforts, in which genomics and bioinformatics are coupled with breeding efforts, will enhance the efficiency and success in breeding crop species for biofuel feedstock use and contributing to the increased use of renewable energy sources.
 
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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
 
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Current Funding Support
Unraveling the heterozygosity, allelic composition, and copy number variation of potato; NSF; 10/1/12-9/30/16
 
Improving the value of plant pathogen genome sequences through uniform, updated and value-added annotation; USDA; 9/01/09-8/31/13
 
Understanding the mechanisms that define cereals: unraveling the function of lineage specific genes within the Poaceae; 9/01/09-8/31/13
 
Development of genetic resources for improvement of American ginseng; MSU AgBioResearch; 5/1/11-6/30/13
 
Identifying differences in abiotic stress gene networks between lowland and upland ecotypes of switchgrass; DOE; 9/1/12-8/31/15
 
The Impact of Pack-MULEs on plant genome evolution and mechanisms of sequence acquisition; NSF; 9/01/11-8/31/15
 
Transferring Research from Model Systems (TRMS): Elucidating the Genetic Architecture of ProVitamin A and Vitamin E Biosynthesis in Seed; NSF; 6/15/10-6/14/15
 
SolCAP: Translating Solanaceae sequence diversity and trait variation into applied outcomes through integrative research, education, and extension; USDA; 10/01/09-9/30/13
 
Precise gene modification for potato improvement; MSU AgBioResearch; 5/1/12-6/30/14
 
Analysis of endogenous variation for biofuel traits in maize & Translational research and breeding in switchgrass: Using maize as a model discovery engine; DOE-GLBRC; 12/01/08-11/30/13

 
Select Publications
Yeo, Y.-S., Nybo, S.E., Chittiboyina, A.G., Weerasooriya, A.D., Wang, Y.-H., Góngora‐Castillo, E., Vaillancourt, B., Buell, C. R., DellaPenna, D.,  Celiz, M.D., Jones, A.D., Wurtele, E.S., RansomN., Dudareva, N., Shabaan, K.A., Tibrewal, N., Chandra, S., Smillie, T., Khan, I.A., Coates, R.M.,Watt, D.S., and Chappell, J. 2013. Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis.  JBC, in press.
 
Góngora-Castillo, E., Childs, K.L., Fedewa, G., Hamilton, J.P., Liscombe, D.K. Magallanes,  M., Mandadi, K.K., Nims, E., Runguphan, W., Vaillancourt, B., Varbanova-Herde, M., DellaPenna,  D., McKnight, T.D., O’Connor, S., and C. R. Buell. 2013. Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PLoS ONE, in press. 
 
C. N. Hirsch and C. R. Buell. 2013. Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes. Annual Review of Plant Biology, in press.

Góngora-Castillo, E., Fedewa, G., Yeo, Y., Chappell, J., DellaPenna, D., and C. R. Buell. 2012. Genomic approaches for interrogating the biochemistry of medicinal plant species. Methods in Enzymology 517: 139-159.
 
Gong, Z., Wu, Y., Koblížková, A., Torres, G.A., Wang, K., Iovene, M., Neumann, P., Zhang, W., Novák, P., Buell, C.R., Macas, J., and J Jiang. 2012. Genome-wide characterization of DNA sequences associated with CENH3 nucleosomes reveals centromere evolution in Solanum species. The Plant Cell 24: 3559–3574.
 
Sekhon, R.S., Childs, K.L., Santoro, N., Foster, C.E., Buell, C.R., de Leon, N., and Kaeppler, S.M. 2012. Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. Plant Physiology 159(4):1730-44.
 
Sim, S. –C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Van Deynze, A., Stoffel, K., Hamilton, J. P., Buell, C. R., Zarka, D., Douches, D. S., Causse M., Vijratne, S., and D. M. Francis. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato (Solanum lycopersicum L.). PLoS ONE 7(7): e40563. doi:10.1371/journal.pone.0040563
 
Felcher, K., Coombs, J., Massa, A.N., Hansey, C., Hamilton, J. P., Veilleux, R., Buell, C. R. and D. Douches. 2012. Integration of two diploid potato linkage maps with the potato physical map. PLoS ONE 7(4): e36347. doi:10.1371/journal.pone.0036347
 
Savory, E. A., Adhikari, B. N., Hamilton, J. P., Vaillancourt, B., Buell, C. R., and B. Day. 2012. mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection. PLoS ONE 7: e35796. doi:10.1371/journal.pone.0035796
 
Davidson, R.M., Gowda, M., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S.-H., Jiang, N., and C. R. Buell. 2012. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. The Plant Journal 71: 492-502.
 
Savory, E., Zou, C., Adhikari, B.,  Hamilton, J. P., Buell, C. R., Shiu, S.-H., and B. Day. 2012. Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death. PLoS ONE 7(4): e34701. doi:10.1371/journal.pone.0034701.
 
Adhikari, B. N., Savory, E. A., Vaillancourt, B., Childs, K. L., Hamilton, J. P., Day, B. and C. R. Buell. 2012. Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis. PLoS ONE 7(4): e34954. doi:10.1371/journal.pone.0034954.
 
Hansey, C.N., Vaillancourt, B., Sekhon, R. S., De Leon, N., Kaeppler, S. M., and C. R. Buell. 2012. Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS ONE (3): e33071.  doi:10.1371/journal.pone.0033071.
 
Hamilton, J. P., Sim, S. –C., Stoffel, K., Van Deynze, A., De Jong, W.S., Douches, D. S., Buell, C. R., and D. M. Francis. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. 2012. The Plant Genome 5: 17-29.
 
Hamilton, J. P. and C. R. Buell. 2012. Advances in Plant Genome Sequencing. The Plant Journal 70:177-190.
 
Childs, K. L., Konganti, K., and Buell, C. R. 2012. The Biofuel Feedstock Genomics Resource: A web-based portal and database to enable functional genomics of plant biofuel feedstock species. Database doi: 10.1093/database/bar061
 
Casler, M.D., Tobias, C.M., Kaeppler, S.M., Buell, C.R., Wang, Z. –Y., Cao, P., Schmutz, J., and P. Ronald. 2011. The Switchgrass Genome: Tools and Strategies. The Plant Genome 4:273-282.
 
Hamilton, J.P., Neeno-Eckwall, E., Adhikari, B., Perna, N., Tisserat, N., Leach, J.E., Lévesque, C. A., and C. R. Buell. 2011. The Comprehensive Phytopathogen Genomics Resource: An electronic resource for data-mining plant pathogen genomes. Database, doi: 10.1093/database/bar053.
 
Massa, A. N., Childs, K. L., Lin, H., Bryan, G. J., Giuliano, G., and Buell, C. R. 2011. The transcriptome of the reference potato genome Solanum tuberosum Group Phureja Clone DM1-3 516R44. PLoSONE 6: e26801.
 
Davidson, R. M., Hansey, C.N., Gowda, M., Childs, K. L., Lin, H., Vaillancourt, B., Sekhon, R.S., de Leon, N., Kaeppler, S., Jiang, N., and Buell, C. R. 2011. Utility of RNA-seq for analysis of maize reproductive transcriptomes. The Plant Genome 4:191-203.
 
Childs, K.L., Davidson, R., and Buell. C. R. 2011. Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE 6(7):e22196.

 
Hamilton, J.P., Hansey, C.N., Whitty, B.R., Stoffel, K., Massa, A.N., Van Deynze, A. De Jong, W.S., Douches, D.S., and Buell, C. R. 2011. Single Nucleotide Polymorphism discovery in elite North American potato germplasm. BMC Genomics 12:302.
 
The Potato Genome Sequencing Consortium. (C. R. Buell is a corresponding author). 2011. Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195.

Iovene, M., Cavagnaro, P.F., Senalik, D., Buell, C.R., Jiang, J., Simon, P.W. 2011. Comparative FISH mapping of Daucus species (Apiaceae). Chromosome Res. 19(4):493-506

Torres, G.A., Gong, Z., Marina Iovene, M., Cory D. Hirsch, C.D., Buell, C.R., Bryan, G.J., Petr Novák, P., Jiří Macas, J., and Jiang, J. 2011. Organization and evolution of subtelomeric DNA in the potato genome. G3 1:85-92.

Triplett, L.R., Hamilton, J., Buell, C.R., Tisserat, N.A., Verdier, V., Zink, F., and Leach, J.E. 2011. Genomic analysis of Xanthomonas oryzae from U.S. rice reveals substantial divergence from known X. oryzae Pathovars. Applied and Environmental Microbiology 77:3930-3937.

Giddings, L.-A., Liscombe, D.K., Hamilton, J. P., Childs, K. L., DellaPenna, D., Buell, C. R., and O’Connor, S. E. 2011. A stereoselective hydroxylation step of alkaloid biosynthesis by a unique cytrochrome P450 in Catharanthus roseus. J Biol Chem 286:16751-16757

Sekhon, R., Lin, H., Childs, K., Hansey, C., Buell, C.R., de Leon, N., and Kaeppler, S. 2011. Genome-wide atlas of transcription through maize development. The Plant Journal 66:553-563.
 
Buell, C. R. and Last, R. L. 2010. Twenty-First Century Plant Biology: Impacts of the Arabidopsis genome on plant biology and agriculture. Plant Physiology 154: 497-500.

Bhaskar, P.B., Wu, L. Busse, J. S., Whitty, B.R., Hamernik, A. J., Jansky, S.H., Buell, C. R., Bethke, P. C., and Jiang, J. 2010. Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato. Plant Physiology 154:939-948.
 
Lévesque, C. A., Brouwer, H., Cano, L., Hamilton, J. P., Holt, C., Huitema, E., Raffaele, S., Robideau, G. P., Thines, M., Win, J., Zerillo, M. M., Beakes, G. W., Boore, J. L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S. I., Gachon, C. M.M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R.H.Y., Johnson, J., Krajaejun, T., Lin, H., Meijer, H.J.G., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Shetty, J., Stajich, J. E., Trripathy, S., Wawra, S., van West, P., Whitty, B. R., Coutinho, P. M., Henrissat, B., Martin, F., Thimas, P. D., Tyler, B. M., De Vries, R. P., Kamoun, S., Yandell, M., Tisserat, N., and Buell, C. R. 2010. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11:R73.

Lou, Q., Iovene, M., Spooner, D. M., Buell, C. R. and J. Jiang. 2010. Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping. Chromosoma 119:435-442.

Lin, H., Moghe, G., Ouyang, S., Iezzoni, A., Shiu, S., Gu, X., and Buell, C. R. 2010. Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol. Biol. 10:41.

Lang, J. M., Hamilton, J., Diaz, M. G. Q., Van Sluys, M. A., Burgos, M. R. G., Vera Cruz, C. M., Buell, C. R., Tisserat, N. A. and Leach, J. E.  2010. Genomics-based diagnostic marker development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.  Plant Disease 94: 311-319.
 
Rhee,Y., Lin, H., Buell, C. R., Childs, K., and Kaeppler, S. 2009. A c2 allele of maize identified in regenerant-derived progeny from tissue culture results from insertion of a novel transposon. Maydica 54:429-437.
 
Zou, C., Lehti-Shiu, M. D., Thibaud-Nissen, F., Prakash, T., Buell, C. R., and Shiu, S. -H.  Evolutionary and expression signatures of pseudogenes in Arabidopsis thaliana and rice. 2009. Plant Physiology 151:3-15.
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 10:317.
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.
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