J. Chris Pires
Associate Professor of Biological Sciences
PhD, 2000 University of Wisconsin - Madison
|Office:||371B Christopher S. Bond Life Sciences Center|
Systematics, phylogenetics, and genome evolution of polyploidy plants
Research descriptionResearch in our lab broadly encompasses plant evolutionary biology—from phylogenetic studies in plant diversity to genome-wide analyses of gene expression. Current investigations are directed at molecular systematics and comparative genomics (phylogenomics), with a particular focus on the evolution and ecology of polyploid plants. Polyploidy, the process of genome doubling that gives rise to organisms with multiple sets of chromosomes is a major evolutionary force in both plants and animals. More than 70% of flowering plants have had at least one polyploid event in their lineage. Many important crop plants—such as alfalfa, cotton, potato, and wheat—are obvious polyploids while others—such as maize, soybean, and cabbage—retain the vestiges of ancient polyploid events. My leading conceptual questions pertain to the consequences of genome doubling, such as deciphering the mechanisms that give rise to novel morphological or ecological features found in polyploids. Understanding the pattern of how such novelty might arise requires an understanding of the evolutionary history of polyploid plants and their diploid relatives. We have two ongoing research projects that synthesize evolutionary and genomic approaches:
1. Polyploidy and phenotypic evolution in Brassica. The genus Brassica (cabbage, broccoli, cauliflower, canola) is a fascinating model for plant domestication because of its spectacular variation in vegetative forms and dynamic chromosomal behavior. Using a phylogenetically informed approach, we are dissecting the reticulate evolutionary history of Brassica. In addition to looking at natural polyploids, we are studying synthetic polyploids to understand the mechanisms that can give rise to novel phenotypes. Recently, we found that resynthesized Brassica napus allopolyploids rapidly evolved heritable differences in flowering time by chromosomal rearrangements. We are following up on this experiment by “replaying the evolutionary tape” to find out if 50 resynthesized polyploid Brassica lines are similar to each other and to natural polyploids. To date, it appears that chromosomal rearrangements and epigenetic events may play a major and previously unsuspected role in the generation of new phenotypes in polyploids. Witnessing the interplay between immediate epigenetic changes and long-term functional gene divergence should provide data to advance our theoretical understanding of the relationship between genome duplication and gene expression. Integrating phylogenetic and genomic approaches will allow us to investigate the dynamics of polyploid evolution.
2. Phylogeny and chromosomal evolution in the Asparagales. We have completed large-scale phylogenetic analyses of the monocot order Asparagales (onions, asparagus, irises, orchids). This work has integrated classical and modern approaches to plant systematics, and based on morphological and molecular data we have discovered surprising phylogenetic results. These discoveries have led to a revised taxonomic classification of the monocots and give us new hypotheses for examining the morphological diversity, historical biogeography, and wide range of genome size and chromosome number of the monocots. To further address these issues, we are utilizing resources being developed for model crop species (e.g., Allium, Asparagus) to analyze genomes in related organisms (e.g., Agave, Brodiaea, irises, orchids). Such studies will synergistically examine the evolution of nuclear genes and chromosomes across the Asparagales and the monocots. Unraveling the complex relationships between genotype and phenotype is one of the most intriguing challenges in evolutionary biology and confronting these questions requires the synthesis of diverse approaches to the study of plant evolution.
Johnson, M.T.J., Carpenter, E.J., Tian, Z., Bruskiewich, R., Burris, J.N., Carrigan, C.T., Chase, M.W., Clarke, N.D., Covshoff, S., dePamphilis, C.W., Edger, P.P., Goh, F., Graham, S., Greiner, S., Hibberd, J.M., Jordon-Thaden, I., Kutchan, T.M., Leebens-Mack, J., Melkonian, M., Miles, N, Myburg, H., Patterson, J., Pires, J.C., Ralph, P., Rolf, M., Sage, R.F., Soltis, D., Soltis, P., Stevenson, D., Stewart, C.N., Surek, B., Thomsen, C.J.M., Villarreal, J.C., Wu, X., Zhang, Y., Deyholos, M.K., and Wong, G.K-S. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS ONE 7: e50226.
Arias, T. and Pires, J.C. 2012. A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications. Taxon 61: 980-988
Witzig, S. B., Freyermuth, S. K., Siegel, M. A., Izci, K., and Pires, J. C. 2012. Is DNA alive? A study of conceptual change through targeted instruction. Research in Science Education DOI 10.1007/s11165-012-9311-4
Bekaert, M. Edger, P.P., Hudson, C.M., Pires, J.C. and G.C. Conant. 2012. Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytologist 196: 596-605
The International Arabidopsis Informatics Consortium. 2012. Taking the next step: Building an Arabidopsis Information Portal. Plant Cell 24: 2248-2256.
Heneen, W.K., Gelata, M., Brismar, K., Xiong, Z, Pires, J.C., Hasterok, R., Stoute, A.I., Scott, R.J., King, G.J. and Smita, K. 2012. Seed colour loci, homoeology and linkage groups of the C-genome chromosomes revealed in Brassica rapa – B. oleracea monosomic alien addition lines. Annals of Botany 109: 1227-1242. 7. * Schnable, J.C., Wang, X., Pires, J.C., and Freeling
Schnable, J.C., Wang, X., Pires, J.C., and Freeling, M. 2012. Escape from preferential retention following repeated whole genome duplications in plants. Frontiers in Plant Science 3: 94.
Seberg, O., Petersen, G., Davis, J.I., Pires, J.C., Stevenson, D.W., Chase, M.W., Fay, M.F., Devey, D.S., Jorgensen, T., Sytsma, K.J., and Pillon, Y. 2012. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. American Journal of Botany 99: 875-889
Van de Peer, Y., and Pires, J.C. 2012. Getting up to speed. Current Opinion in Plant Biology 15: 111-114.
Reneker, J., Lyons, E., Conant, G.C., Pires, J.C., Freeling, M., Shyu, C-R., and Korkin, D. 2012. Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences, U.S.A. 109 (19): E1183-E1191.
Matsushita, S., Tyagi, A., Pires, J.C., and Madlung, A. 2012. Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids. Genetics 191: 535-547.
Tang, H., Woodhouse, M.R., Cheng, F., Schnable, J.C., Pedersen, B.S., Conant, G., Wang, X., Freeling, M., and Pires, J.C. 2012. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190: 1563-1574
Jiao, Y., Leebens-Mack, J., Ayyampalayam, S., Bowers, J.E., McKain, M.R., McNeal, J., Rolf, M., Ruzicka, D.R., Wafula, E., Wickett, N.J., Wu, X., Zhang, Y., Wang, J., Zhang, Y., Carpenter, E.J., Deyholos, M.K., Kutchan, T.M., Chanderbali, A.S., Soltis, P.S., Stevenson, D.W., McCombie, R., Pires, J.C., Wong, G.K-S., Soltis, D.E., and dePamphilis, C.W. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: art. No R3.
McKain, M.R., Wickett, N.J., Zhang, Y., Ayyampalayam, S, McCombie, W.R., Chase, M.W., Pires, J.C., dePamphilis, C.W., and Leebens-Mack, J. 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karytoypes in Agavoideae (Asparagaceae). American Journal of Botany 99: 397-406. Invited paper for special issue on “Methods and Applications of Next-Generation Sequencing in Botany.”
Steele, P.R., Hertweck, K.L., Mayfield, D., McKain, M.R, Leebens-Mack, J., and Pires, J.C. 2012 Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae. American Journal of Botany 99: 330-348
Hudson C.M., Puckett, E.E., Bekaert, M., Pires, J.C. and Conant, G.C. 2011. Selection for higher gene copy number after different types of plant gene duplications. Genome Biology and Evolution doi: 10.1093/gbe/evr115
Xiong, Z., Gaeta, R.T. and J. C. Pires. 2011. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. PNAS 108: 7908-7913.
Steele, P.R., and J. C. Pires. 2011. Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification. American Journal of Botany 98: 415-425.
The Brassica rapa Genome Sequencing Project Consortium. 2011. The genome of the mesoploid crop species Brassica rapa. Nature Genetics 43: 1035-1039.
Xiong, Z., and J. C. Pires. 2011. Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors. Genetics 187: 37-49.
Galbraith, D.W., Bennetzen, J.L., Kellogg, E.A. Pires, J.C., and Soltis, P.S. 2011. The Genomes of All Angiosperms: A Call for a Coordinated Global Census. Journal of Botany doi: 10.1155/2011/646198
Wang, X., Torres, M.J., Pierce, G., Lemke, C., Nelson, L.K., Yuksel, B., Bowers, J.E., Marler, B., Xiao, Y., Lin, L., Epps, E., Sarazen, H., Rogers, C., Karunakaran, S., Ingles, J., Giattina, E., Mun, J.H., Seol, Y.J., Park, B.S., Amasino, R. M., Quiros, C.F., Osborn, T.C., Pires, J.C., Town, C. and Paterson, A.H. 2011. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics 12: 740.
Bachtrog, D., Kirkpatrick, M., Mank, J.E., McDaniel, S.F., Pires, J.C., Rice, W., and Valenzuela, N. 2011. Are all sex chromosomes created equal? Trends in Genetics 9: 350-357.
Bekaert, M. Edger, P.P., Pires, J.C. and Conant, G.C. 2011. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23: 1719-1728.
Zou, J. Fu, D., Gong, H, Qian, W, Xia, W, Pires, J.C., Li, R.Y., Long Y., Mason, A.S. Yang T.J., Lim, Y.P., Park, B.S. and Meng, J. 2011. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. Plant Journal 68: 212- 224.
Zuccolo, A., Bowers, J.E., Estill, J.C., Xiong, Z., Luo, M., Sebastian, A., Goicoechea, J.L., Collura, K., Yu, Y., Jiao, Y., Duarte, J., Tang, H., Ayyampalayam, S., Rounsley, S., Kudrna, D., Paterson, A.H., Pires, J.C., Chanderbali, A., Soltis, D.E., Chamala, S., Barbazuk, B., Soltis, P.S., Albert, V.A., Ma, H., Mandoli, D., Banks, J., Carlson, J.E., Tomkins, J. dePamphilis, C.W., Wing, R.A., and Leebens-Mack, J. 2011. A physical map of the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology 12: R48.
Mayfield, D., Chen, Z. J. and Pires, J. C. 2011. Epigenetic regulation of flowering time in polyploids. Current Opinion in Plant Biology 14: 174-178
Halverson, K.L., Pires, J. C. and Abell, S.K. 2011. Exploring the complexity of tree thinking expertise in an undergraduate plant systematics course. Science Education 95: 794-823.
Raven, P.H. Chase, J.M., and Pires, J. C. 2011. Introduction to special issue on biodiversity. American Journal of Botany 98: 333-335.
Xiong, Z., and Pires, J. C. 2011. Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors. Genetics 187: 37-49.
Xiong, Z., Kim, J. S., and Pires, J. C. 2010. Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Cytogenetic and Genome Research 129: 190-198.
Gaeta, R.T. and Pires, J. C. 2010. Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytologist 186: 18-28.
Navabi, Z.K., Parkin, I.A.P., Pires, J.C., Xiong, Z., Thiagarajah, M.R., Good, A.G., and Rahman, J.M. 2010.Introgression of B-genome chromosomes in a doubled haploid interspecific population of Brassica napus x B. carinata. Genome 53: 619-629.
Duarte, J.M, Wall, P.K., Edger, P.P., Landherr, L.L., Ma, H., Pires, J.C., Leebens-Mack, J. and dePamphilis, C.W. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10: 61 doi:10.1186/1471-2148-10-61.
Givnish, T. J., Ames, M., McNeal, J. R., McKain, M.R., Steele, P. R., dePamphilis, C. W., Graham, S. W., Pires, J. C., Stevenson, D. W., Zomlefer, W. B., Briggs, B. G., Duvall, M. R., Moore, M. J., Heaney, J. M., Soltis, D. E., Soltis, P. S., Thiele, K., and Leebens-Mack, J. H. 2010. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Garden 97: 584-616.
Oct. 16, 2013
Researchers create first genetic map of non-coding DNA in plants
June 7, 2013
2013 Outstanding Undergraduate Research Mentor Award given to Dr. Chris Pires
June 3, 2013
Visiting high schoolers get a lesson in ‘tree thinking’ from Dr. Pires
April 26, 2013
Chris Pires recognized with Advising Shout Out! Award
April 8, 2013
Three Biology Undergraduates Recognized by National Science Foundation
April 10, 2012
Identical DNA Codes Found in Plant Species Provides Insights into Plant and Animal Evolution