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J. Chris Pires

J. Chris Pires

Professor, Biological Sciences

Phone: 573-882-0619
piresjc@missouri.edu
371b Bond Life Science Center

Pires studies the evolution of plants. He does this by comparing the genetic material of plants that are known to regularly duplicate their chromosomes. This process, known as whole genome duplication, can give rise to new plant types and traits. He creates the equivalent of a “family tree” for these plant species, which he then uses to discover how this duplication influenced their evolutions. Pires works with plants in the genus Brassica, which includes cabbage, broccoli, cauliflower, and canola, and Asparagales, which includes onions, asparagus, irises and orchids. He recently discovered that chromosomes within canola can rearrange themselves in unexpected ways during meiosis, a stage during which cells divide to form pollen or eggs. In addition to shedding light on plant evolution, his research may be used to develop new or more valuable crops.

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News about J. Chris Pires

Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. New Phytologist; 230(1):372-386.

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Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. Bird KA, Niederhuth CE, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. New Phytologist; 230(1):354-371.

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Feralization: Confronting the Complexity of Domestication and Evolution. Mabry ME, Rowan TN, Pires JC, Decker JE. Trends in Genetics; 37(4):302-305.

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The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype. Arias T, Niederhuth CE, McSteen P, Pires JC. Frontiers in Plant Science; 12:637115.

Featured in this article: Paula McSteen, J. Chris Pires.

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Chromosome inheritance and meiotic stability in allopolyploid Brassica napus. Xiong Z, Gaeta RT, Edger PP, Cao Y, Zhao K, Zhang S, Chris Pires J. G3: Genes, Genomes, Genetics; 11(2):jkaa011.

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Phylogeny and multiple independent whole-genome duplication events in the Brassicales. Mabry ME, Brose JM, Blischak PD, Sutherland B, Dismukes WT, Bottoms CA, Edger PP, Washburn JD, An H, Hall JC, McKain MR, Al-Shehbaz I, Barker MS, Schranz ME, Conant GC, Pires JC. American Journal of Botany; 107(8):1148-1164.

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Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia. Gunn BF, Murphy DJ, Walsh NG, Conran JG, Pires JC, Macfarlane TD, Birch JL. Molecular Phylogenetics and Evolution; 149:106836.

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Current status of the multinational Arabidopsis community. Parry G, Provart NJ, Brady SM, Uzilday B, Adams K, Araújo W, Aubourg S, Baginsky S, Bakker E, Bärenfaller K, Batley J, Beale M, Beilstein M, Belkhadir Y, Mendel G, Berardini T, Bergelson J, Blanco-Herrera F, Brady S, Braun H-P, Briggs S, Brownfield L, Cardarelli M, Castellanos-Uribe M, Coruzzi G, Dassanayake M, De Jaeger G, Dilkes B, Doherty C, Ecker J, Edger P, Edwards D, El Kasmi F, Eriksson M, Exposito-Alonso M, Falter-Braun P, Fernie A, Ferro M, Fiehn O, Friesner J, Greenham K, Guo Y, Hamann T, Hancock A, Hauser M-T, Heazlewood J, Ho C-H, Hõrak H, Huala E, Hwang I, Iuchi S, Jaiswal P, Jakobson L, Jiang Y, Jiao Y, Jones A, Kadota Y, Khurana J, Kliebenstein D, Knee E, Kobayashi M, Koch M, Krouk G, Larson T, Last R, Lepiniec L, Li S, Lurin C, Lysak M, Maere S, Malinowski R, Maumus F, May S, Mayer K, Mendoza-Cozatl D, Mendoza-Poudereux I, Micol JL, Millar H, Mock H-P, Mukhtar K, Mukhtar S, Murcha M, Nakagami H, Nakamura Y, Nicolov L, Nikolau B, Nowack M, Nunes-Nesi A, Palmgren M, Parry G, Patron N, Peck S, Pedmale U, Perrot-Rechenmann C, Pieruschka R, Pío-Beltrán J, Pires JC, Provart N, Rajjou L, Reiser L, Rhee S, Rigas S, Rolland N, Romanowski A, Savaldi-Goldstein S, Schmitz R, Schulze W, Seki M, Shimizu KK, Slotkin K, Small I, Somers D, Sozzani R, Spillane C, Srinivasan R, Taylor N, Tello-Ruiz M-K, Thelen J, Tohge T, Town C, Toyoda T, Uzilday B, Walley J, Ware D, Weckwerth W, Whitelegge J, Wienkoop S, Wright C, Wrzaczek M, Yamazaki M, Yanovsky M, Žárský V, Zhong X, Van De Peer Y, Van Wijk K, Von Gillhaussen P, The Multinational Arabidopsis Steering Committee. Plant Direct; 4(7):e00248.

Featured in this article: David Mendoza-Cózatl, Scott Peck, J. Chris Pires, Jay Thelen.

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Genomic Origin and Diversification of the Glucosinolate MAM Locus. Abrahams RS, Pires JC, Schranz ME. Frontiers in Plant Science; 11:711.

Featured in this article: Shawn Abrahams, J. Chris Pires.

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Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, brassicaceae). Züst T, Strickler SR, Powell AF, Mabry ME, An H, Mirzaei M, York T, Holland CK, Kumar P, Erb M, Petschenka G, Gómez J-M, Perfectti F, Müller C, Pires JC, Mueller LA, Jander G. eLife; 9:e51712.

Featured in this article: Hong An, J. Chris Pires.

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Evolutionary insights into plant breeding. Turner-Hissong SD, Mabry ME, Beissinger TM, Ross-Ibarra J, Pires JC. Current Opinion in Plant Biology; 54:93-100.

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Functional characterization of SMN evolution in mouse models of SMA. Osman EY, Bolding MR, Villalón E, Kaifer KA, Lorson ZC, Tisdale S, Hao Y, Conant GC, Pires JC, Pellizzoni L, Lorson CL. Scientific Reports; 9(1):9472.

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Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. An H, Qi X, Gaynor ML, Hao Y, Gebken SC, Mabry ME, McAlvay AC, Teakle GR, Conant GC, Barker MS, Fu T, Yi B, Pires JC. Nature Communications; 10(1):2878.

Featured in this article: Hong An, J. Chris Pires.

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One thousand plant transcriptomes and the phylogenomics of green plants. Leebens-Mack JH, Barker MS, Carpenter EJ, Deyholos MK, Gitzendanner MA, Graham SW, Grosse I, Li Z, Melkonian M, Mirarab S, Porsch M, Quint M, Rensing SA, Soltis DE, Soltis PS, Stevenson DW, Ullrich KK, Wickett NJ, DeGironimo L, Edger PP, Jordon-Thaden IE, Joya S, Liu T, Melkonian B, Miles NW, Pokorny L, Quigley C, Thomas P, Villarreal JC, Augustin MM, Barrett MD, Baucom RS, Beerling DJ, Benstein RM, Biffin E, Brockington SF, Burge DO, Burris JN, Burris KP, Burtet-Sarramegna V, Caicedo AL, Cannon SB, Çebi Z, Chang Y, Chater C, Cheeseman JM, Chen T, Clarke ND, Clayton H, Covshoff S, Crandall-Stotler BJ, Cross H, dePamphilis CW, Der JP, Determann R, Dickson RC, Di Stilio VS, Ellis S, Fast E, Feja N, Field KJ, Filatov DA, Finnegan PM, Floyd SK, Fogliani B, García N, Gâteblé G, Godden GT, Goh FQY, Greiner S, Harkess A, Heaney JM, Helliwell KE, Heyduk K, Hibberd JM, Hodel RGJ, Hollingsworth PM, Johnson MTJ, Jost R, Joyce B, Kapralov MV, Kazamia E, Kellogg EA, Koch MA, Von Konrat M, Könyves K, Kutchan TM, Lam V, Larsson A, Leitch AR, Lentz R, Li F-W, Lowe AJ, Ludwig M, Manos PS, Mavrodiev E, McCormick MK, McKain M, McLellan T, McNeal JR, Miller RE, Nelson MN, Peng Y, Ralph P, Real D, Riggins CW, Ruhsam M, Sage RF, Sakai AK, Scascitella M, Schilling EE, Schlösser E-M, Sederoff H, Servick S, Sessa EB, Shaw AJ, Shaw SW, Sigel EM, Skema C, Smith AG, Smithson A, Stewart CN Jr, Stinchcombe JR, Szövényi P, Tate JA, Tiebel H, Trapnell D, Villegente M, Wang C-N, Weller SG, Wenzel M, Weststrand S, Westwood JH, Whigham DF, Wu S, Wulff AS, Yang Y, Zhu D, Zhuang C, Zuidof J, Chase MW, Pires JC, Rothfels CJ, Yu J, Chen C, Chen L, Cheng S, Li J, Li R, Li X, Lu H, Ou Y, Sun X, Tan X, Tang J, Tian Z, Wang F, Wang J, Wei X, Xu X, Yan Z, Yang F, Zhong X, Zhou F, Zhu Y, Zhang Y, Ayyampalayam S, Barkman TJ, Nguyen N-P, Matasci N, Nelson DR, Sayyari E, Wafula EK, Walls RL, Warnow T, An H, Arrigo N, Baniaga AE, Galuska S, Jorgensen SA, Kidder TI, Kong H, Lu-Irving P, Marx HE, Qi X, Reardon CR, Sutherland BL, Tiley GP, Welles SR, Yu R, Zhan S, Gramzow L, Theißen G, Wong GK-S, One Thousand Plant Transcriptomes Initiative. Nature; 574(7780):679-685.

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Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers. Grindstaff B, Mabry ME, Blischak PD, Quinn M, Chris Pires J. Applications in Plant Sciences; 7(8):e11280.

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Usability of reference-free transcriptome assemblies for detection of differential expression: A case study on Aethionema arabicum dimorphic seeds. Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA. BMC Genomics; 20(1):95.

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The renaissance of comparative biochemistry. Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. American Journal of Botany; 106(1):3-13.

Featured in this article: Ruthie Angelovici, J. Chris Pires.

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Integrating networks, Phylogenomics, and population genomics for the study of polyploidy. Blischak PD, Mabry ME, Conant GC, Pires JC. Annual Review of Ecology, Evolution, and Systematics; 49(2):253-278.

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Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. American Journal of Botany; 105(11):1888-1910.

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Transcriptome-wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome. Wang J, Cappa JJ, Harris JP, Edger PP, Zhou W, Pires JC, Adair M, Unruh SA, Simmons MP, Schiavon M, Pilon-Smits EAH. Plant Biotechnology Journal; 16(9):1582-1594.

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Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Hurgobin B, Golicz AA, Bayer PE, Chan C-KK, Tirnaz S, Dolatabadian A, Schiessl SV, Samans B, Montenegro JD, Parkin IAP, Pires JC, Chalhoub B, King GJ, Snowdon R, Batley J, Edwards D. Plant Biotechnology Journal; 16(7):1265-1274.

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Erratum: Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses (Scientific reports (2017) 7 1 (13528)). Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC. Scientific Reports; 8(1):7120.

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Genome-wide nucleotide diversity and associations with geography, ploidy level and glucosinolate profiles in Aethionema arabicum (Brassicaceae). Mohammadin S, Wang W, Liu T, Moazzeni H, Ertugrul K, Uysal T, Christodoulou CS, Edger PP, Pires JC, Wright SI, Schranz ME. Plant Systematics and Evolution; 304(5):619-630.

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Topological data analysis as a morphometric method: Using persistent homology to demarcate a leaf morphospace. Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH. Frontiers in Plant Science; 9:553.

Featured in this article: Hong An, Ruthie Angelovici, Clement Bagaza, J. Chris Pires.

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Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). Unruh SA, McKain MR, Lee Y-I, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC. American Journal of Botany; 105(4):631-640.

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Editorial overview: Genome studies and molecular genetics: Treasure troves of evolution. Van de Peer Y, Pires JC. Current Opinion in Plant Biology; 42:iii-v.

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Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC. American Journal of Botany; 105(3):463-469.

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Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC. PLoS Genetics; 14(3):e1007267.

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Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived. Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC. Genome Biology and Evolution; 10(3):999-1011.

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The asparagus genome sheds light on the origin and evolution of a young y chromosome. Harkess A, Zhou J, Xu C, Bowers JE, Van Der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Chen H, Gao J, Mao Z, Pires JC, Luo M, Kudrna D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G. Nature Communications; 8(1):1279.

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Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses. Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC. Scientific Reports; 7(1):13528.

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Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. Hackenberg D, McKain MR, Lee SG, Roy Choudhury S, McCann T, Schreier S, Harkess A, Pires JC, Wong GK-S, Jez JM, Kellogg EA, Pandey S. New Phytologist; 216(2):562-575.

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Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR. Plant Cell; 29(9):2150-2167.

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Molecular resources from transcriptomes in the brassicaceae family. Lopez L, Wolf EM, Pires JC, Edger PP, Koch MA. Frontiers in Plant Science; 8:1488.

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Anatolian origins and diversification of aethionema, the sister lineage of the core brassicaceae. Mohammadin S, Peterse K, van de Kerke SJ, Chatrou LW, Dönmez AA, Mummenhoff K, Pires JC, Edger PP, Al-Shehbaz IA, Schranz ME. American Journal of Botany; 104(7):1042-1054.

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Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Qi X, An H, Ragsdale AP, Hall TE, Gutenkunst RN, Chris Pires J, Barker MS. Molecular Ecology; 26(13):3373-3388.

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Insights into the evolution of hydroxyproline-rich glycoproteins from 1000 plant transcriptomes. Johnson KL, Cassin AM, Lonsdale A, Wong GK-S, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ. Plant Physiology; 174(2):904-921.

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Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Bird KA, An H, Gazave E, Gore MA, Pires JC, Robertson LD, Labate JA. Frontiers in Plant Science; 8:321.

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The Evolution of HD2 Proteins in Green Plants. Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V. Trends in Plant Science; 21(12):1008-1016.

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Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes. Pires JC, Conant GC. Annual Review of Genetics; 50:113-131.

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The pangenome of an agronomically important crop plant Brassica oleracea. Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D. Nature Communications; 7:13390.

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Timing of rapid diversification and convergent origins of active pollination within agavoideae (Asparagaceae). McKain MR, McNeal JR, Kellar PR, Eguiarte LE, Pires JC, Leebens-Mack J. American Journal of Botany; 103(10):1717-1729.

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Retrotransposon proliferation coincident with the evolution of dioecy in asparagus. Harkess A, Mercati F, Abbate L, McKain M, Pires JC, Sala T, Sunseri F, Falavigna A, Leebens-Mack J. G3: Genes, Genomes, Genetics; 6(9):2679-2685.

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Spreading winge and flying high: The evolutionary importance of polyploidy after a century of study. Barker MS, Husband BC, Chris Pires J. American Journal of Botany; 103(7):1139-1145.

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Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae). Burke SV, Wysocki WP, Zuloaga FO, Craine JM, Pires JC, Edger PP, Mayfield-Jones D, Clark LG, Kelchner SA, Duvall MR. BMC Plant Biology; 16(1):140.

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Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie Y, Zhu Y, Carpenter E, Wong GK-S, Stewart CN Jr. BMC Biotechnology; 16(1):47.

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Convergent evolution and the origin of complex phenotypes in the age of systems biology. Washburn JD, Bird KA, Conant GC, Pires JC. International Journal of Plant Sciences; 177(4):305-318.

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Editorial overview: Genome studies and molecular genetics: Of plant genes, genomes, and genomics. Van de Peer Y, Pires JC. Current Opinion in Plant Biology; 30:iv-vi.

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A phylogenomic assessment of ancient polyploidy and genome evolution across the poales. McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, Depamphilis CW, Givnish TJ, Chris Pires J, Stevenson DW, Leebens-Mack JH. Genome Biology and Evolution; 8(4):1150-1164.

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Resolution of brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Huang C-H, Sun R, Hu Y, Zeng L, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP, Pires JC, Tan D-Y, Zhong Y, Ma H. Molecular Biology and Evolution; 33(2):394-412.

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Selecting superior de novo transcriptome assemblies: Lessons learned by leveraging the best plant genome. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Chris Pires J, Leebens-Mack JH, DePamphilis CW. PLoS ONE; 11(1):e0146062.

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Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI. New Phytologist; 209(2):855-870.

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Meeting report: Fungal genomics meets social media: Highlights of the 28th fungal genetics conference at asilomar. Momany M, Di Pietro A, Alexander WG, Barker BM, Harb OS, Kamoun S, Martin F, Chris Pires J, Stajich JE, Thomma BPHJ, Unruh S. G3: Genes, Genomes, Genetics; 5(12):2523-2525.

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Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism. Norup MF, Petersen G, Burrows S, Bouchenak-Khelladi Y, Leebens-Mack J, Pires JC, Linder HP, Seberg O. Molecular Phylogenetics and Evolution; 92:25-44.

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The players may change but the game remains: Network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC, Lamberson WR, Conant GC. Nucleic Acids Research; 43(20):9600-9612.

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Positionally-conserved but sequence-diverged: Identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. Mohammadin S, Edger PP, Pires JC, Schranz ME. BMC Plant Biology; 15(1):217.

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Phylogeny and photosynthesis of the grass tribe Paniceae. Washburn JD, Schnable JC, Davidse G, Pires JC. American Journal of Botany; 102(9):1493-1505.

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Resolving deep relationships of PACMAD grasses: a phylogenomic approach. Cotton JL, Wysocki WP, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield-Jones D, Duvall MR. BMC Plant Biology; 15:178.

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The butterfly plant arms-race escalated by gene and genome duplications. Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC, Blanchette M, Bureau TE, Wright SI, DePamphilis CW, Schranz ME, Barker MS, Conant GC, Wahlberg N, Vogel H, Pires JC, Wheat CW, Berenbaum MR. Proceedings of the National Academy of Sciences of the United States of America; 112(27):8362-8366.

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Biodiversity Comparison among Phylogenetic Diversity Metrics and between Three North American Prairies. Roxanne Kellar P, Ahrendsen DL, Aust SK, Jones AR, Pires JC. Applications in Plant Sciences; 3(7):8.

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Phylogenetics, divergence times and diversification from three genomic partitions in monocots. Hertweck KL, Kinney MS, Stuart SA, Maurin O, Mathews S, Chase MW, Gandolfo MA, Pires JC. Bontanical Journal of the Linnean Society; 178(3):375-393.

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Elucidating steroid alkaloid biosynthesis in Veratrum californicum: Production of verazine in Sf9 cells. Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A, Wong GK-S, Deyholos MK, Edger PP, Pires JC, Leebens-Mack JH, Mann DA, Kutchan TM. Plant Journal; 82(6):991-1003.

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Plastid phylogenomics of the cool-season grass subfamily: Clarification of relationships among early-diverging tribes. Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. AoB PLANTS; 7(1).

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Unreduced gametes: Meiotic mishap or evolutionary mechanism?. Mason AS, Pires JC. Trends in Genetics; 31(1):5-10.

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Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. Molecular Biology and Evolution; 31(12):3095-3112.

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Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C, Wong GKS, Bowman JL. Molecular Phylogenetics and Evolution; 81:159-173.

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Nonadditive gene expression in polyploids. Yoo M-J, Liu X, Pires JC, Soltis PS, Soltis DE. Annual Review of Genetics; 48:485-517.

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Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP. Mitochondrion; 19(PB):135-143.

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Erratum: Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome (Science (2014) 345:6199 (950-953)). Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier M-C, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee T-H, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma, J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury J-M, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Science; 345(6202).

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A multi-step comparison of short-read full plastome sequence assembly methods in grasses. Wysocki WP, Clark LG, Kelchner SA, Burke SV, Pires JC, Edger PP, Mayfield DR, Triplett JK, Columbus JT, Ingram AL, Duvall MR. Taxon; 63(4):899-910.

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Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier M-C, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee T-H, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma, J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury J-M, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Science; 345(6199):950-953.

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Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution. Delaux P-M, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané J-M. PLoS Genetics; 10(7):e1004487.

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Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the brassicaceae (mustards). Edger PP, Tang M, Bird KA, Mayfield DR, Conant G, Mummenhoff K, Koch MA, Pires JC. PLoS ONE; 9(7):e101341.

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Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Parkin IAP, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Chris Pires J, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG. Genome Biology; 15(6):R77.

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Phylogenomics of the plant family Araceae. Henriquez CL, Arias T, Pires JC, Croat TB, Schaal BA. Molecular Phylogenetics and Evolution; 75(1):91-102.

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Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time. Conant GC, Birchler JA, Pires JC. Current Opinion in Plant Biology; 19:91-98.

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The brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang T-J, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park B-S, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee T-H, Wang J, Jin H, Li Z, Li X, Zhang J, Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. Nature Communications; 5:3930.

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Current perspectives and the future of domestication studies. Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Vigueira CC, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MTP, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, De Casas RR, Sanjur OI, Thomas MG, Fuller DQ. Proceedings of the National Academy of Sciences of the United States of America; 111(17):6139-6146.

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Storytelling and story testing in domestication. Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, De Casas RR, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MTP, Larson G, Thomas MG. Proceedings of the National Academy of Sciences of the United States of America; 111(17):6159-6164.

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Erratum: 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 (5283-5288)). Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. Proceedings of the National Academy of Sciences of the United States of America; 111(17):6527.

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Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. Proceedings of the National Academy of Sciences of the United States of America; 111(14):5283-5288.

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Systematics and evolution of inflorescence structure in the tradescantia alliance (commelinaceae). Hertweck KL, Pires JC. Systematic Botany; 39(1):105-116.

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Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. Arias T, Beilstein MA, Tang M, McKain MR, Pires JC. American Journal of Botany; 101(1):86-91.

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Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric Schranz M. Genome Biology and Evolution; 5(11):2155-2173.

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An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandáková T, Lysak MA, Van Den Bergh E, Schranz ME, Harrison PM, Moses AM. Nature Genetics; 45(8):891-898.

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Is DNA Alive? A Study of Conceptual Change Through Targeted Instruction. Witzig SB, Freyermuth SK, Siegel MA, Izci K, Pires JC. Research in Science Education; 43(4):1361-1375.

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Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales. Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC. Seminars in Cell and Developmental Biology; 24(4):320-331.

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Molecular systematics of Allium subgenus Amerallium (Amaryllidaceae) in North America. Wheeler EJ, Mashayekhi S, Mcneal DW, Travis Columbus J, Chris Pires J. American Journal of Botany; 100(4):701-711.

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The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the paleohexaploid Brassica rapa. Subramaniam S, Wang X, Freeling M, Pires JC. Genome Biology and Evolution; 5(4):646-660.

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Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes. Johnson MTJ, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN, Surek B, Thomsen CJM, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK-S. PLoS ONE; 7(11):e50226.

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A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications. Arias T, Chris Pires J. Taxon; 61(5):980-988.

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Metabolic and evolutionary costs of herbivory defense: Systems biology of glucosinolate synthesis. Bekaert M, Edger PP, Hudson CM, Pires J, Conant GC. New Phytologist; 196(2):596-605.

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Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapaB. oleracea monosomic alien addition lines. Heneen WK, Geleta M, Brismar K, Xiong Z, Pires JC, Hasterok R, Stoute AI, Scott RJ, King GJ, Kurup S. Annals of Botany; 109(7):1227-1242.

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Allopolyploidization lays the foundation for evolution of distinct populations: Evidence from analysis of synthetic arabidopsis allohexaploids. Matsushita SC, Tyagi AP, Thornton GM, Pires JC, Madlung A. Genetics; 191(2):535-547.

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Escape from preferential retention following repeated whole genome duplications in plants. Schnable JC, Wang X, Pires JC, Freeling M. Frontiers in Plant Science; 3(MAY):94.

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Long identical multispecies elements in plant and animal genomes. Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu C-R, Korkin D. Proceedings of the National Academy of Sciences of the United States of America; 109(19):E1183-E1191.

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Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. Seberg O, Petersen G, Davis JI, Chris Pires J, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y. American Journal of Botany; 99(5):875-889.

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Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC. Genetics; 190(4):1563-1574.

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Getting up to speed. Van de Peer Y, Pires JC. Current Opinion in Plant Biology; 15(2):111-114.

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Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). McKain MR, Wickett N, Zhang Y, Ayyampalayam S, Richard McCombie W, Chase MW, Chris Pires J, DePamphilis CW, Leebens-Mack J. American Journal of Botany; 99(2):397-406.

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Quality and quantity of data recovered from massively parallel sequencing: Examples in asparagales and Poaceae. Roxanne Steele P, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Chris Pires J. American Journal of Botany; 99(2):330-348.

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Selection for higher gene copy number after different types of plant gene duplications. Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC. Genome Biology and Evolution; 3(1):1369-1380.

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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. Zou J, Fu D, Gong H, Qian W, Xia W, Pires JC, Li R, Long Y, Mason AS, Yang T-J, Lim YP, Park BS, Meng J. Plant Journal; 68(2):212-224.

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The genome of the mesopolyploid crop species Brassica rapa. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park B-S, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim J-S, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S-J, Choi S-R, Lee T-H, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. Nature Genetics; 43(10):1035-1040.

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A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. Wang X, Torres MJ, Pierce G, Lemke C, Nelson LK, Yuksel B, Bowers JE, 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 RM, Quiros CF, Osborn TC, Pires JC, Town C, Paterson AH. BMC Genomics; 12:470.

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Are all sex chromosomes created equal?. Bachtrog D, Kirkpatrick M, Mank JE, McDaniel SF, Pires JC, Rice WR, Valenzuela N. Trends in Genetics; 27(9):350-357.

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Exploring the complexity of tree thinking expertise in an undergraduate systematics course. Halverson KL, Pires CJ, Abell SK. Science Education; 95(5):794-823.

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A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J. Genome Biology; 12(5):R48.

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Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Xiong Z, Gaeta RT, Pires JC. Proceedings of the National Academy of Sciences of the United States of America; 108(19):7908-7913.

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Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Bekaert M, Edger PP, Chris Pires J, Conant GC. Plant Cell; 23(5):1719-1728.

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Epigenetic regulation of flowering time in polyploids. Mayfield D, Chen ZJ, Pires JC. Current Opinion in Plant Biology; 14(2):174-178.

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Analysis of B-genome chromosome introgression in interspecific hybrids of Brassica napus x B. carinata. Navabi ZK, Stead KE, Pires JC, Xiong Z, Sharpe AG, Parkin IAP, Rahman MH, Good AG. Genetics; 187(3):659-673.

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Introduction to special issue on biodiversity. Raven PH, Chase JM, Chris Pires J. American Journal of Botany; 98(3):333-335.

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Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification. Roxanne Steele P, Chris Pires J. American Journal of Botany; 98(3):415-425.

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Contrasting patterns of support among plastid genes and genomes for major clades of the monocotyledons. Davis JI, McNeal JR, Barrett CF, Chase MW, Cohen JI, Duvall MR, Givnish TJ, Graham SW, Petersen G, Pires JC, Seberg O, Stevenson DW, Leebens-Mack J. Early Events in Monocot Evolution; 315-349.

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Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors. Xiong Z, Chris Pires J. Genetics; 187(10:37-49.

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Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales. Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, Depamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, Soltis PS, Thiele K, Leebens-Mack JH. Annals of the Missouri Botanical Garden; 97(4):584-616.

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Introgression of B-genome chromosomes in a doubled haploid population of brassica napus × B. carinata. Navabi ZK, Parkin IAP, Pires JC, Xiong Z, Thiagarajah MR, Good AG, Rahman MH. Genome; 53(8):619-629.

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Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Xiong Z, Kim JS, Pires JC. Cytogenetic and Genome Research; 129(1-3):190-198.

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Preface. Birchler JA, Pires JC. Cytogenetic and Genome Research; 129(1-3):5.

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Homoeologous recombination in allopolyploids: The polyploid ratchet. Gaeta RT, Chris Pires J. New Phytologist; 186(1):18-28.

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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, Depamphilis CW. BMC Evolutionary Biology; 10(1):61.

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Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. Trick M, Kwon S-J, Choi SR, Fraser F, Soumpourou E, Drou N, Wang Z, Lee SY, Yang T-J, Mun J-H, Paterson AH, Town CD, Pires JC, Pyo Lim Y, Park B-S, Bancroft I. BMC Genomics; 10:539.

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Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen K, Cooper A, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim J-J, Kim KS, Sonstegard TS, Van Tassell CP, Neibergs HL, McEwan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, McClure MC, Rolf MM, Kim J, Schnabel RD, Taylor JF. Proceedings of the National Academy of Sciences of the United States of America; 106(44):18644-18649.

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Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae). Wright KM, Pires JC, Madlung A. American Journal of Botany; 96(9):1656-1664.

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Comparative analysis between homoeologous genome segments of brassica napus and its progenitor species reveals extensive sequence-level divergence. Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Chris Pires J, Paterson AH, Town C, Bancroft I. Plant Cell; 21(7):1912-1928.

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Gene and genome duplications: The impact of dosage-sensitivity on the fate of nuclear genes. Edger PP, Pires JC. Chromosome Research; 17(5):699-717.

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Analysis of gene expression in resynthesized Brassica napus allopolyploids using arabidopsis 70mer oligo microarrays. Gaeta RT, Yoo S-Y, Pires JC, Doerge RW, Chen ZJ, Osborn TC. PLoS ONE; 4(3):e4760.

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Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR. PLoS ONE; 3(10):e3353.

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A renaissance of cytogenetics: Studies in polyploidy and chromosomal evolution. Pires JC, Hertweck KL. Annals of the Missouri Botanical Garden; 95(2):275-281.

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Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. Plant Cell; 19(11):3403-3417.

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Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus. Telgmann-Rauber A, Jamsari A, Kinney MS, Pires JC, Jung C. Molecular Genetics and Genomics; 278(3):221-234.

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Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA). Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, DePamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu Y-L, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. OMICS A Journal of Integrative Biology; 10(2):231-237.

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Evolutionary history of the angiosperms and its relevance to Brassica. Paterson AH, Bowers JE, Estill JC, Osborn TC, Pires JC, Amasino R, Quiros CF, Farnham M. Acta Horticulturae; 706:49-53.

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Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T. Plant Physiology; 140(1):336-348.

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Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: Evidence from an ndhF phylogeny. Givnish TJ, Pires JC, Graham SW, McPherson MA, Prince LM, Patterson TB, Rai HS, Roalson EH, Evans TM, Hahn WJ, Millam RC, Meerow AW, Molvray M, Kores PJ, O'Brien HE, Hall JC, Kress WJ, Sytsma KJ. Proceedings of the Royal Society B: Biological Sciences; 272(1571):1481-1490.

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Rapid concerted evolution of nuclear ribosomal DNA in two tragopogon allopolyploids of recent and recurrent origin. Kovarik A, Pires JC, Leitch AR, Lim KY, Sherwood AM, Matyasek R, Rocca J, Soltis DE, Soltis PS. Genetics; 169(2):931-944.

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Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. Walling JG, Pires JC, Jackson SA. Methods in Enzymology; 395:443-460.

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The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Chen ZJ, Wang J, Tian L, Lee H-S, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B, Lippman Z, Vaughn M, Pires JC, Colot V, Doerge RW, Martienssen RA, Comai L, Osborn TC. Biological Journal of the Linnean Society; 82(4):689-700.

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Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC. Biological Journal of the Linnean Society; 82(4):675-688.

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Genome redundancy and plasticity within ancient and recent Brassica crop species. Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC. Biological Journal of the Linnean Society; 82(4):665-674.

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Recent and recurrent polyploidy in Tragopogon (Asteraceae): Cytogenetic, genomic and genetic comparisons. Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate JA, Mavrodiev E. Biological Journal of the Linnean Society; 82(4):485-501.

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Clades, clocks, and continents: Historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the Southern Hemisphere. Sytsma KJ, Litt A, Zjhra ML, Pires JC, Nepokroeff M, Conti E, Walker J, Wilson PG. International Journal of Plant Sciences; 165(4 SUPPL.):S85-S105.

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Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors. Pires JC, Lim KY, Kovarík A, Matyásek R, Boyd A, Leitch AR, Leitch IJ, Bennett MD, Soltis PS, Soltis DE. American Journal of Botany; 91(7):1022-1035.

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Ancient vicariance or recent long-distance dispersal? Inferences about phylogeny and South American-African disjunctions in rapateaceae and bromeliaceae based on ndhF sequence data. Givnish TJ, Millam KC, Evans TM, Hall JC, Pires JC, Berry PE, Sytsma KJ. International Journal of Plant Sciences; 165(4):S35-S54.

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Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Lee H-S, Wang J, Tian L, Jiang H, Black MA, Madlung A, Watson B, Lukens L, Pires JC, Wang JJ, Comai L, Osborn TC, Doerge RW, Chen ZJ. Plant Biotechnology Journal; 2(1):45-57.

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Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Hass BL, Pires JC, Porter R, Phillips RL, Jackson SA. Theoretical and Applied Genetics; 107(5):773-782.

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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bremer B, Bremer K, Chase MW, Reveal JL, Soltis DE, Soltis PS, Stevens PF, Anderberg AA, Fay MF, Goldblatt P, Judd WS, Källersjö M, Kårehed J, Kron KA, Lundberg J, Nickrent DL, Olmstead RG, Oxelman B, Pires JC, Rodman JE, Rudall PJ, Savolainen V, Sytsma KJ, Van Der Bank M, Wurdack K, Xiang JQ-Y, Zmarzty S. Bontanical Journal of the Linnean Society; 141(4):399-436.

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Understanding mechanisms of novel gene expression in polyploids. Osborn TC, Chris Pires J, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA. Trends in Genetics; 19(3):141-147.

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Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data. Levin RA, Wagner WL, Hoch PC, Nepokroeff M, Pires JC, Zimmer EA, Sytsma KJ. American Journal of Botany; 90(1):107-115.

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Urticalean rosids: Circumscription, rosid ancestry, and phylogenetics based on rbcL, trnL-F, and ndhF sequences. Sytsma KJ, Morawetz J, Chris Pires J, Nepokroeff M, Conti E, Zjhra M, Hall JC, Chase MW. American Journal of Botany; 89(9):1531-1546.

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A phylogenetic evaluation of a biosystematic framework: Brodiaea and related petaloid monocots (Themidaceae). Pires JC, Sytsma KJ. American Journal of Botany; 89(8):1342-1359.

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Plant systematics in the next 50 years – Re-mapping the new frontier. Sytsma KJ, Pires JC. Taxon; 50(3):713-732.

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Dragnet Ecology—“Just the Facts, Ma’am”: The Privilege of Science in a Postmodern World: Science of intrinsic quality needs narratives with explicit values—not just facts—particularly as it faces multiple-level complexity in advising on environmental policy, such as planning for energy futures. Allen TFH, Tainter JA, Chris Pires J, Hoekstra TW. BioScience; 51(6):475-486.

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New infraspecific names in North American Liliales. Kiger RW, Case FW Jr, Pires JC. Taxon; 50(1):201.

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Molecular and morphological phylogenetic analyses of Themidaceae (Asparagales). Pires JC, Fay MF, Davis WS, Hufford L, Rova J, Chase MW, Sytsma KJ. Kew Bulletin; 56(3):601-626.

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Polyphyly and Convergent Morphological Evolution in Commelinales and Commelinidae: Evidence from rbcL Sequence Data. Givnish TJ, Evans TM, Pires JC, Sytsma KJ. Molecular Phylogenetics and Evolution; 12(3):360-385.

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