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.
Huang CH, Sun RR, Hu Y, Zeng LP, Zhang N, Cai LM, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP et al: Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution. Molecular Biology and Evolution 2016, 33(2):394-412.
Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang YT, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW: Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. Plos One 2016, 11(1).
Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L et al: Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytologist 2016, 209(2):855-870.
Mason, A.S., and Pires, J.C. 2015. Unreduced gametes: meiotic mishap or evolutionary mechanism? Trends in Genetics 31:5-10.
Augustin, M.M., Ruzicka, D.R., Shukla, A.K., Augustin, J.M., Starks, C.M., O'Neil-Johnson, M., McKain, M.R., Evans, B.S., Barrett, M.D., Smithson, A., Wong, G.K.-S., Deyholos, M.K., Edger, P.P., Pires, J.C., Leebens-Mack, J.H., Mann, D.A., Kutchan, T.M., 2015. Elucidating steroid alkaloid biosynthesis in Veratrum californicum: Production of verazine in Sf9 cells. Plant Journal, 82:991-1003.
Washburn JD, Schnable JC, Davidse G, Pires JC: Phylogeny and photosynthesis of the grass tribe Paniceae. American Journal of Botany 2015, 102(9):1493-1505.
Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC et al: The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Research 2015, 43(20):9600-9612.
Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR et al: Plastid phylogenomics of the cool-season grass subfamily: Clarification of relationships among early-diverging tribes. AoB PLANTS 2015, 7(1).
Roxanne Kellar P, Ahrendsen DL, Aust SK, Jones AR, Pires JC: Biodiversity Comparison among Phylogenetic Diversity Metrics and between Three North American Prairies. Applications in Plant Sciences 2015, 3(7).
Norup MF, Petersen G, Burrows S, Bouchenak-Khelladi Y, Leebens-Mack J, Pires JC, Linder HP, Seberg O: Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism. Molecular Phylogenetics and Evolution 2015, 92:25-44.
Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Pires JC, Stajich JE, Thomma B et al: Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar. G3-Genes Genomes Genetics 2015, 5(12):2523-2525.
Mohammadin S, Edger PP, Pires JC, Schranz ME: Positionally-conserved but sequence-diverged: Identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. BMC Plant Biology 2015, 15(1).
Mason AS, Pires JC: Unreduced gametes: Meiotic mishap or evolutionary mechanism? Trends in Genetics 2015, 31(1):5-10.
Hertweck KL, Kinney MS, Stuart SA, Maurin O, Mathews S, Chase MW, Gandolfo MA, Pires JC: Phylogenetics, divergence times and diversification from three genomic partitions in monocots. Botanical Journal of the Linnean Society 2015, 178(3):375-393.
Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M et al: The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences of the United States of America 2015, 112(27):8362-8366.
Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield-Jones D, Duvall MR: Resolving deep relationships of PACMAD grasses: A phylogenomic approach. BMC Plant Biology 2015, 15(1).
Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A et al: Elucidating steroid alkaloid biosynthesis in Veratrum californicum: Production of verazine in Sf9 cells. Plant Journal 2015, 82(6):991-1003.
Hertweck KL, Pires JC: Systematics and evolution of inflorescence structure in the tradescantia alliance (commelinaceae). Systematic Botany 2014, 39(1):105-116.
Arias T, Beilstein MA, Tang M, McKain MR, Pires JC: Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. American Journal of Botany 2014, 101(1):86-91.
Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C: Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution 2014, 31(12):3095-3112.
Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH et al: Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Molecular Phylogenetics and Evolution 2014, 81:159-173.
Yoo MJ, Liu X, Pires JC, Soltis PS, Soltis DE: Nonadditive gene expression in polyploids. In: Annual Review of Genetics. vol. 48; 2014: 485-517.
Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP: Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion 2014, 19(PB):135-143.
Wysocki WP, Clark LG, Kelchner SA, Burke SV, Pires JC, Edger PP, Mayfield DR, Triplett JK, Columbus JT, Ingram AL et al: A multi-step comparison of short-read full plastome sequence assembly methods in grasses. Taxon 2014, 63(4):899-910.
Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B et al: Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Science 2014, 345(6199):950-953.
Parkin IAP, Koh C, Tang HB, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL et al: Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 2014, 15(6):18.
Edger PP, Tang M, Bird KA, Mayfield DR, Conant G, Mummenhoff K, Koch MA, Pires JC: Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the brassicaceae (mustards). PLoS ONE 2014, 9(7).
Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution. PLoS Genetics 2014, 10(7).
Conant GC, Birchler JA, Pires JC: Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology 2014, 19:91-98.
Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, Huang S et al: The brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 2014, 5.
Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X: Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(14):5283-5288.
Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Vigueira CC, Denham T, Dobney K et al: Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(17):6139-6146.
Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L et al: Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(17):6159-6164.
Henriquez CL, Arias T, Pires JC, Croat TB, Schaal BA: Phylogenomics of the plant family Araceae. Molecular Phylogenetics and Evolution 2014, 75(1):91-102.
Hertweck, K., and Pires, J.C. 2014. Systematics and evolution of inflorescence structure in the Tradescantia alliance (Commelinaceae). Systematic Botany 39: 105-116.
Witzig SB, Freyermuth SK, Siegel MA, Izci K, Pires JC: Is DNA Alive? A Study of Conceptual Change Through Targeted Instruction. Research in Science Education 2013, 43(4):1361-1375.
Hofberger JA, Lyons E, Edger PP, Pires JC, Schranz ME: Whole Genome and Tandem Duplicate Retention Facilitated Glucosinolate Pathway Diversification in the Mustard Family. Genome Biology and Evolution 2013, 5(11):2155-2173.
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM et al: An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics 2013, 45(8):891-898.
Wheeler EJ, Mashayekhi S, McNeal DW, Travis Columbus J, Chris Pires J: Molecular systematics of Allium subgenus Amerallium (Amaryllidaceae) in North America. American Journal of Botany 2013, 100(4):701-711.
Subramaniam S, Wang X, Freeling M, Pires JC: The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the paleohexaploid Brassica rapa. Genome Biology and Evolution 2013, 5(4):646-660.
Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC: Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales. Seminars in Cell and Developmental Biology 2013, 24(4):320-331.
Johnson MTJ, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW et al: Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes. PLoS ONE 2012, 7(11).
Arias T, Chris Pires J: A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications. Taxon 2012, 61(5):980-988.
Bekaert M, Edger PP, Hudson CM, Pires J, Conant GC: Metabolic and evolutionary costs of herbivory defense: Systems biology of glucosinolate synthesis. New Phytologist 2012, 196(2):596-605.
The International Arabidopsis Informatics Consortium. 2012. Taking the next step: Building an Arabidopsis Information Portal. Plant Cell 24: 2248-2256.
Heneen WK, Geleta M, Brismar K, Xiong ZY, Pires JC, Hasterok R, Stoute AI, Scott RJ, King GJ, Kurup S: 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 2012, 109(7):1227-1242.
Schnable JC, Wang X, Pires JC, Freeling M: Escape from preferential retention following repeated whole genome duplications in plants. Frontiers in Plant Science 2012, 3(MAY).
Seberg O, Petersen G, Davis JI, Chris Pires J, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ et al: Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. American Journal of Botany 2012, 99(5):875-889.
Van de Peer Y, Pires JC: Getting up to speed. Current Opinion in Plant Biology 2012, 15(2):111-114.
Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D: Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America 2012, 109(19):E1183-E1191.
Matsushita SC, Tyagi AP, Thornton GM, Pires JC, Madlung A: Allopolyploidization lays the foundation for evolution of distinct populations: Evidence from analysis of synthetic arabidopsis allohexaploids. Genetics 2012, 191(2):535-547.
Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC: Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 2012, 190(4):1563-1574.
Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ et al: A genome triplication associated with early diversification of the core eudicots. Genome Biology 2012, 13(1).
McKain MR, Wickett N, Zhang Y, Ayyampalayam S, Richard McCombie W, Chase MW, Chris Pires J, DePamphilis CW, Leebens-Mack J: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 2012, 99(2):397-406.
Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Chris Pires J: Quality and quantity of data recovered from massively parallel sequencing: Examples in asparagales and Poaceae. American Journal of Botany 2012, 99(2):330-348.
Heneen WK, Geleta M, Brismar K, Xiong Z, Pires JC, Hasterok R, Stoute AI, Scott RJ, King GJ, Kurup S: Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapaB. oleracea monosomic alien addition lines. Annals of Botany 2012, 109(7):1227-1242.
Honors & Awards
Selected honors and awards
Ann K. Covington Award, MU Fellowships Office 2016
MU Advising Shout Out Award 2013
University of Missouri Outstanding Undergraduate Research Mentor Award 2013
Margaret Menzel Award, Botanical Society of America Outstanding Paper 2009
University of Missouri Outstanding Undergraduate Research Mentor Award 2008
May 3, 2016
April 13, 2016
MU Biology students shine in 2016 NSF Graduate Research Fellowship competition
Jan. 27, 2016
Aug. 26, 2015
July 19, 2015
June 30, 2015
June 29, 2015
Genetic study of co-evolution could provide clues to better food production
June 29, 2015
Dec. 3, 2014
Sept. 3, 2014
Scientists Discover the Genomic Origins of Canola
June 3, 2014
Jacob Washburn receives grants to study evolution of photosynthesis in grasses
April 3, 2014
Sarah Unruh awarded NSF Graduate Research Fellowship
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