Michael Purugganan

Plant evolutionary genomics

Evolutionary and ecological genomics of plant adaptations

We study the evolutionary forces that act in plant developmental networks at the species level, and in mapping and isolating genes that underlie natural variation in that are responsible for plant adaptation. We are also interested in exploring the “ecological transciptome” – the dynamic gene networks found in plants in ecological environments. This work combines concepts and techniques in evolutionary and quantitative genomics, developmental biology, evolutionary ecology, and computational biology.

Genetics of Plant Domestication

Crops are plant species that have evolved in a cultural context to provide food and other products for human society. Crop species are fascinating subjects for evolutionary study, since they are examples of species that have undergone rapid diversification under intense selection pressures. They also permit us to understand the dynamic interface between genetics, evolution and human culture. We are studying the evolution of genes in rice (Oryza sativa). By using tools of molecular and evolutionary genomics, these studies provide insights into the processes and mechanisms that accompany cultural selection on plant species during domestication events.

The Evolution of Multicellularity and Social Behaviour

The model protist Dictyostelium discoideum has been a model for the study of social biology as well as the evolution of multicellularity. We are integrating techniques and approaches in population genetics, genomics, systems biology and glycomics to study kin discrimination and recognition in this social microbe.

Work in my laboratory is funded by grants from the NSF Plant Genome Research program and the Population and Evolutionary Processes program.

Carlos Bustamante (Stanford), Barbara Schaal (Washington University), Scott Jackson (University of Georgia), Richard Bonneau (NYU), Kourosh-Salehi Ashtiani (NYU Abu Dhabi), Endang Septiningsih (International Rice Research Institute)

Dr. Michael Purugganan received his B.S. in Chemistry from the University of the Philippines (1985), an M.A. from Columbia University (1986) and a Ph.D. in Botany with a Global Policy minor at the University of Georgia (1993). After obtaining his Ph.D., he did postdoctoral research as an Alfred P. Sloan Molecular Evolution Fellow at the University of California in San Diego, studying the evolution of development (1993-1995). Dr. Purugganan is a leader in the field of evolutionary and ecological genomics and his work focuses on identifying the molecular basis for evolutionary adaptations that occur in nature. Prior to joining the NYU faculty in 2006, he was the William Neal Reynolds Distinguished Professor of Genetics at North Carolina State University, where he also won the Outstanding Faculty Research Award and the Sigma Xi Research Prize. He is the recipient of an Alfred P. Sloan Foundation Young Investigator Award, a Guggenheim Fellowship, is a Kavli Fellow, and in 2005 was elected a Fellow of the American Association for the Advancement of Science. Dr. Purugganan is on the editorial boards of the journals Genome Biology and Evolution, Molecular Ecology, Trends in Plant Science and the Annual Review of Ecology, Evolution and Systematics.

American Association for the Advancement of Science

Genetics Society of America and Society for Molecular Biology and Evolution

Date of these PubMed search results: March 24 2020
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1. The strength and pattern of natural selection on gene expression in rice.
   Nature (2020 Feb) PMID: 32051590
   Groen SC, Calic I, Joly‑Lopez Z, Platts AE, Choi JY, Natividad M, Dorph K, Mauck WM 3rd, Bracken B, Cabral CLU, Kumar A, Torres RO, Satija R, Vergara G, Henry A, Franks SJ, Purugganan MD
2. An inferred fitness consequence map of the rice genome.
   Nat Plants (2020 Feb) PMID: 32042156
   Joly‑Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD
3. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.
   Genome Biol (2020 Feb 5) PMC7001208 free full-text archive
   Choi JY, Lye ZN, Groen SC, Dai X, Rughani P, Zaaijer S, Harrington ED, Juul S, Purugganan MD
4. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.
   PLoS Genet (2020 Jan) PMC7004385 free full-text archive
   Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ
5. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island.
   Mol Biol Evol (2020 Mar 1) PMC7038655 free full-text archive
   Choi JY, Purugganan M, Stacy EA
6. Genome-wide association mapping of date palm fruit traits.
   Nat Commun (2019 Oct 15) PMC6794320 free full-text archive
   Hazzouri KM, Gros‑Balthazard M, Flowers JM, Copetti D, Lemansour A, Lebrun M, Masmoudi K, Ferrand S, Dhar MI, Fresquez ZA, Rosas U, Zhang J, Talag J, Lee S, Kudrna D, Powell RF, Leitch IJ, Krueger RR, Wing RA, Amiri KMA, Purugganan MD
7. The bracteatus pineapple genome and domestication of clonally propagated crops.
   Nat Genet (2019 Oct) PMID: 31570895
   Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Huang L, Wang H, Hwa TY, Kao SM, Choi JY, Sharma A, Song J, Wang L, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung CW, Wang ML, Coppens d'Eeckenbrugge G, Sanewski GM, Purugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R
8. Evolutionary Insights into the Nature of Plant Domestication.
   Curr Biol (2019 Jul 22) PMID: 31336092
   Purugganan MD
9. The complex geography of domestication of the African rice Oryza glaberrima.
   PLoS Genet (2019 Mar) PMC6424484 free full-text archive
   Choi JY, Zaidem M, Gutaker R, Dorph K, Singh RK, Purugganan MD
10. Copy Number Variation in Domestication.
    Trends Plant Sci (2019 Apr) PMID: 30745056
    Lye ZN, Purugganan MD
11. Cross-species hybridization and the origin of North African date palms.
    Proc Natl Acad Sci U S A (2019 Jan 29) PMC6358688 free full-text archive
    Flowers JM, Hazzouri KM, Gros‑Balthazard M, Mo Z, Koutroumpa K, Perrakis A, Ferrand S, Khierallah HSM, Fuller DQ, Aberlenc F, Fournaraki C, Purugganan MD
12. Evolutionary and ecological functional genomics, from lab to the wild.
    Plant J (2019 Jan) PMID: 30444573
    Zaidem ML, Groen SC, Purugganan MD
13. The rice genome revolution: from an ancient grain to Green Super Rice.
    Nat Rev Genet (2018 Aug) PMID: 29872215
    Wing RA, Purugganan MD, Zhang Q
14. Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism.
    Front Plant Sci (2018) PMC5826053 free full-text archive
    Hazzouri KM, Khraiwesh B, Amiri KMA, Pauli D, Blake T, Shahid M, Mullath SK, Nelson D, Mansour AL, Salehi‑Ashtiani K, Purugganan M, Masmoudi K
15. Multiple Origin but Single Domestication Led to Oryza sativa.
    G3 (Bethesda) (2018 Mar 2) PMC5844301 free full-text archive
    Choi JY, Purugganan MD
16. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice.
    Mol Biol Evol (2018 Feb 1) PMC5850837 free full-text archive
    Choi JY, Purugganan MD
17. The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.
    Mol Biol Evol (2017 Apr 1) PMC5400379 free full-text archive
    Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, Purugganan MD
18. Systems genetics of plant adaptation to environmental stresses.
    Am J Bot (2016 Dec) PMID: 27864265
    Groen SC, Purugganan MD
19. Tracing ancestor rice of Suriname Maroons back to its African origin.
    Nat Plants (2016 Oct 3) PMID: 27694825
    van Andel TR, Meyer RS, Aflitos SA, Carney JA, Veltman MA, Copetti D, Flowers JM, Havinga RM, Maat H, Purugganan MD, Wing RA, Schranz ME
20. EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.
    Plant Cell (2016 Oct) PMC5134975 free full-text archive
    Wilkins O, Hafemeister C, Plessis A, Holloway‑Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish SV, Septiningsih EM, Bonneau R, Purugganan M
21. Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment.
    G3 (Bethesda) (2016 Oct 13) PMC5068935 free full-text archive
    Yuan W, Flowers JM, Sahraie DJ, Purugganan MD
22. Domestication history and geographical adaptation inferred from a SNP map of African rice.
    Nat Genet (2016 Sep) PMID: 27500524
    Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, Dorph K, Barretto A, Gross B, Fuller DQ, Bimpong IK, Ndjiondjop MN, Hazzouri KM, Gregorio GB, Purugganan MD
23. Extreme QTL mapping of germination speed in Arabidopsis thaliana.
    Mol Ecol (2016 Sep) PMID: 27454560
    Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD
24. Developing maps of fitness consequences for plant genomes.
    Curr Opin Plant Biol (2016 Apr) PMID: 26950251
    Joly‑Lopez Z, Flowers JM, Purugganan MD
25. Evolution of Plant Phenotypes, from Genomes to Traits.
    G3 (Bethesda) (2016 Apr) PMC4825648 free full-text archive
    Casacuberta JM, Jackson S, Panaud O, Purugganan M, Wendel J
26. Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis.
    Plant J (2016 Feb) PMC4815425 free full-text archive
    Rest JS, Wilkins O, Yuan W, Purugganan MD, Gurevitch J
27. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.
    Elife (2015 Nov 26) PMC4718725 free full-text archive
    Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Muller C, Septiningsih EM, Bonneau R, Purugganan M
28. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.
    Nat Commun (2015 Nov 9) PMC4667612 free full-text archive
    Hazzouri KM, Flowers JM, Visser HJ, Khierallah HSM, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD
29. Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.
    Plant Cell (2015 Sep) PMC4815094 free full-text archive
    Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EF, Salehi‑Ashtiani K, Purugganan MD
30. Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress.
    Physiol Plant (2015 Sep) PMID: 26082319
    Pires IS, Negrao S, Oliveira MM, Purugganan MD
31. An evolutionary genomic tale of two rice species.
    Nat Genet (2014 Sep) PMID: 25162803
    Purugganan MD
32. Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum.
    BMC Genomics (2014 Jul 21) PMC4118049 free full-text archive
    Li SI, Buttery NJ, Thompson CR, Purugganan MD
33. Current perspectives and the future of domestication studies.
    Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035915 free full-text archive
    Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo‑Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, Rubio de Casas R, Sanjur OI, Thomas MG, Fuller DQ
34. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record.
    Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035951 free full-text archive
    Fuller DQ, Denham T, Arroyo‑Kalin M, Lucas L, Stevens CJ, Qin L, Allaby RG, Purugganan MD
35. Storytelling and story testing in domestication.
    Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035932 free full-text archive
    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, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MT, Larson G, Thomas MG
36. Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS.
    Nat Commun (2014 Apr 16) PMC3997802 free full-text archive
    Rosas U, Mei Y, Xie Q, Banta JA, Zhou RW, Seufferheld G, Gerard S, Chou L, Bhambhra N, Parks JD, Flowers JM, McClung CR, Hanzawa Y, Purugganan MD
37. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).
    Mol Biol Evol (2014 Apr) PMC3969568 free full-text archive
    Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, Locklear S, Concepcion GP, Purugganan MD
38. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms.
    Rice (N Y) (2013 Oct 28) PMC3874672 free full-text archive
    Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, Flowers JM, Purugganan MD, Nakamura I, Sato Y, Sato T, Crayn D, Simon B, Waters DL, Henry RJ, Ishikawa R
39. Evolution of crop species: genetics of domestication and diversification.
    Nat Rev Genet (2013 Dec) PMID: 24240513
    Meyer RS, Purugganan MD
40. Plasticity regulators modulate specific root traits in discrete nitrogen environments.
    PLoS Genet (2013) PMC3764102 free full-text archive
    Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD
41. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
    BMC Genomics (2013 Aug 28) PMC3844514 free full-text archive
    Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, Qi XT, Guo XS, Zhang L, He WM, Chang RZ, Liang QS, Guo Y, Ye C, Wang XB, Tao Y, Guan RX, Wang JY, Liu YL, Jin LG, Zhang XQ, Liu ZX, Zhang LJ, Chen J, Wang KJ, Nielsen R, Li RQ, Chen PY, Li WB, Reif JC, Purugganan M, Wang J, Zhang MC, Wang J, Qiu LJ
42. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
    Proc Natl Acad Sci U S A (2013 Sep 10) PMC3773737 free full-text archive
    Rosas U, Cibrian‑Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM
43. Different evolutionary histories of two cation/proton exchanger gene families in plants.
    BMC Plant Biol (2013 Jul 4) PMC3726471 free full-text archive
    Pires IS, Negrao S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD
44. Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina.
    Dev Cell (2013 Apr 15) PMC3660048 free full-text archive
    Thanawala SU, Rister J, Goldberg GW, Zuskov A, Olesnicky EC, Flowers JM, Jukam D, Purugganan MD, Gavis ER, Desplan C, Johnston RJ Jr
45. Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.
    Ecol Evol (2012 Jun) PMC3402192 free full-text archive
    Samis KE, Murren CJ, Bossdorf O, Donohue K, Fenster CB, Malmberg RL, Purugganan MD, Stinchcombe JR
46. Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.
    Mol Ecol (2012 Sep) PMID: 22646149
    Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, Purugganan MD, Schaal BA
47. Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana.
    Ecol Lett (2012 Aug) PMID: 22583905
    Banta JA, Ehrenreich IM, Gerard S, Chou L, Wilczek A, Schmitt J, Kover PX, Purugganan MD
48. Genome-wide patterns of Arabidopsis gene expression in nature.
    PLoS Genet (2012) PMC3330097 free full-text archive
    Richards CL, Rosas U, Banta J, Bhambhra N, Purugganan MD
49. The plant proteome folding project: structure and positive selection in plant protein families.
    Genome Biol Evol (2012) PMC3318447 free full-text archive
    Pentony MM, Winters P, Penfold‑Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD
50. Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice.
    Mol Biol Evol (2012 Feb) PMID: 21917724
    Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD
51. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.
    PLoS One (2011) PMC3108957 free full-text archive
    Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD
52. Molecular evidence for a single evolutionary origin of domesticated rice.
    Proc Natl Acad Sci U S A (2011 May 17) PMC3101000 free full-text archive
    Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD
53. The cooperative amoeba: Dictyostelium as a model for social evolution.
    Trends Genet (2011 Feb) PMID: 21167620
    Li SI, Purugganan MD
54. Plant phenotypic plasticity in a changing climate.
    Trends Plant Sci (2010 Dec) PMID: 20970368
    Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M
55. Migration, isolation and hybridization in island crop populations: the case of Madagascar rice.
    Mol Ecol (2010 Nov) PMID: 20964753
    Mather KA, Molina J, Flowers JM, Rubinstein S, Rauh BL, Lawton‑Rauh A, Caicedo AL, McNally KL, Purugganan MD
56. Laboratory markers of cardiovascular risk in pediatric SLE: the APPLE baseline cohort.
    Lupus (2010 Oct) PMC4049625 free full-text archive
    Ardoin SP, Schanberg LE, Sandborg C, Yow E, Barnhart HX, Mieszkalski Kl, Ilowite NT, von Scheven E, Eberhard A, Levy DM, Kimura Y, Silverman E, Bowyer SL, Punaro L, Singer NG, Sherry DD, McCurdy D, Klein‑Gitelman M, Wallace C, Silver R, Wagner‑Weiner L, Higgins GC, Brunner HI, Jung LK, Imundo L, Soep JB, Reed AM
57. Archaeological data reveal slow rates of evolution during plant domestication.
    Evolution (2011 Jan) PMID: 20666839
    Purugganan MD, Fuller DQ
58. Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum.
    PLoS Genet (2010 Jul 1) PMC2895654 free full-text archive
    Flowers JM, Li SI, Stathos A, Saxer G, Ostrowski EA, Queller DC, Strassmann JE, Purugganan MD
59. MicroRNAs in plants: Possible contributions to phenotypic diversity.
    Plant Signal Behav (2008 Oct) PMC2634387 free full-text archive
    Ehrenreich IM, Purugganan M
60. Population genomics of the Arabidopsis thaliana flowering time gene network.
    Mol Biol Evol (2009 Nov) PMID: 19625391
    Flowers JM, Hanzawa Y, Hall MC, Moore RC, Purugganan MD
61. A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana.
    PLoS Genet (2009 Jul) PMC2700969 free full-text archive
    Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R
62. Candidate gene association mapping of Arabidopsis flowering time.
    Genetics (2009 Sep) PMC2746157 free full-text archive
    Ehrenreich IM, Hanzawa Y, Chou L, Roe JL, Kover PX, Purugganan MD
63. Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana.
    Mol Ecol (2009 Jul) PMID: 19457201
    Reininga JM, Nielsen D, Purugganan MD
64. The nature of selection during plant domestication.
    Nature (2009 Feb 12) PMID: 19212403
    Purugganan MD, Fuller DQ
65. Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster.
    Mol Biol Evol (2009 Mar) PMID: 19139056
    Caicedo AL, Richards C, Ehrenreich IM, Purugganan MD
66. The evolution of plant genomes: scaling up from a population perspective.
    Curr Opin Genet Dev (2008 Dec) PMID: 19131240
    Flowers JM, Purugganan MD
67. A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons.
    Science (2008 Aug 8) PMID: 18687965
    Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, Sari MA, Collin F, Flowers JM, Pitrat M, Purugganan MD, Dogimont C, Bendahmane A
68. Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
    Plant Physiol (2008 Apr) PMC2287364 free full-text archive
    Ehrenreich IM, Purugganan MD
69. Independent origins of self-compatibility in Arabidopsis thaliana.
    Mol Ecol (2008 Jan) PMID: 18179433
    Shimizu KK, Shimizu‑Inatsugi R, Tsuchimatsu T, Purugganan MD
70. Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World.
    Genetics (2007 Nov) PMC2147987 free full-text archive
    Saisho D, Purugganan MD
71. The extent of linkage disequilibrium in rice (Oryza sativa L.).
    Genetics (2007 Dec) PMC2219496 free full-text archive
    Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD
72. Genome-wide patterns of nucleotide polymorphism in domesticated rice.
    PLoS Genet (2007 Sep) PMC1994709 free full-text archive
    Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel‑Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD
73. Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae).
    Mol Ecol (2007 Oct) PMID: 17784920
    Lawton‑Rauh A, Robichaux RH, Purugganan MD
74. Genetics of microenvironmental canalization in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A (2007 Aug 21) PMC1959448 free full-text archive
    Hall MC, Dworkin I, Ungerer MC, Purugganan M
75. The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping.
    Genetics (2007 Jun) PMC1894586 free full-text archive
    Ehrenreich IM, Stafford PA, Purugganan MD
76. Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field.
    Am Nat (2007 May) PMID: 17427127
    Korves TM, Schmid KJ, Caicedo AL, Mays C, Stinchcombe JR, Purugganan MD, Schmitt J
77. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.
    PLoS Genet (2006 Nov 17) PMC1636696 free full-text archive
    Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI
78. Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae).
    Genetica (2007 May) PMID: 16924407
    Fan C, Xiang QY, Remington DL, Purugganan MD, Wiegmann BM
79. The molecular genetic basis of plant adaptation.
    Am J Bot (2006 Jul) PMID: 21642159
    Ehrenreich IM, Purugganan MD
80. Epialleles via DNA methylation: consequences for plant evolution.
    Trends Ecol Evol (2004 Jun) PMID: 16701276
    Kalisz S, Purugganan MD
81. Comparative sequencing of plant genomes: choices to make.
    Plant Cell (2006 May) PMC1456863 free full-text archive
    Jackson S, Rounsley S, Purugganan M
82. Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus.
    Appl Environ Microbiol (2006 Apr) PMC1449082 free full-text archive
    Miller SR, Purugganan MD, Curtis SE
83. Selection under domestication: evidence for a sweep in the rice waxy genomic region.
    Genetics (2006 Jun) PMC1526538 free full-text archive
    Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD
84. Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae): the effects of latitude and FLC variation.
    Am J Bot (2005 Oct) PMID: 21646087
    Stinchcombe JR, Caicedo AL, Hopkins R, Mays C, Boyd EW, Purugganan MD, Schmitt J
85. Evolutionary and ecological genomics of Arabidopsis.
    Plant Physiol (2005 Jun) PMC1150378 free full-text archive
    Shimizu KK, Purugganan MD
86. Comparative plant genomics. Frontiers and prospects.
    Plant Physiol (2005 Jun) PMC1150366 free full-text archive
    Caicedo AL, Purugganan MD
87. High-diversity genes in the Arabidopsis genome.
    Genetics (2005 Aug) PMC1449776 free full-text archive
    Cork JM, Purugganan MD
88. The evolutionary dynamics of plant duplicate genes.
    Curr Opin Plant Biol (2005 Apr) PMID: 15752990
    Moore RC, Purugganan MD
89. The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome.
    Mol Ecol (2005 Jan) PMID: 15643950
    Tsompana M, Abad J, Purugganan M, Moyer JW
90. Darwinian selection on a selfing locus.
    Science (2004 Dec 17) PMID: 15604405
    Shimizu KK, Cork JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Awadalla P, Purugganan MD
91. Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae).
    Mol Phylogenet Evol (2004 Dec) PMID: 15522789
    Fan C, Purugganan MD, Thomas DT, Wiegmann BM, Xiang JQ
92. Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.
    Proc Natl Acad Sci U S A (2004 Nov 2) PMC524852 free full-text archive
    Caicedo AL, Stinchcombe JR, Olsen KM, Schmitt J, Purugganan MD
93. The evolution of plant development.
    Am J Bot (2004 Oct) PMID: 21652320
    Friedman WE, Moore RC, Purugganan MD
94. Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana.
    Mol Biol Evol (2005 Jan) PMID: 15371526
    Moore RC, Grant SR, Purugganan MD
95. Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles.
    Genetics (2004 Jul) PMC1470957 free full-text archive
    Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD
96. The evolution of molecular genetic pathways and networks.
    Bioessays (2004 May) PMID: 15112228
    Cork JM, Purugganan MD
97. A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA.
    Proc Natl Acad Sci U S A (2004 Mar 30) PMC384812 free full-text archive
    Stinchcombe JR, Weinig C, Ungerer M, Olsen KM, Mays C, Halldorsdottir SS, Purugganan MD, Schmitt J
98. The early stages of duplicate gene evolution.
    Proc Natl Acad Sci U S A (2003 Dec 23) PMC307628 free full-text archive
    Moore RC, Purugganan MD
99. Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana.
    Genetics (2003 Sep) PMC1462760 free full-text archive
    Ungerer MC, Halldorsdottir SS, Purugganan MD, Mackay TF
100. Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana.
     Genetics (2003 Sep) PMC1462755 free full-text archive
     Weinig C, Dorn LA, Kane NC, German ZM, Halldorsdottir SS, Ungerer MC, Toyonaga Y, Mackay TF, Purugganan MD, Schmitt J
101. Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae).
     Mol Ecol (2003 May) PMID: 12694292
     Lawton‑Rauh A, Robichaux RH, Purugganan MD
102. Merging ecology, molecular evolution, and functional genetics.
     Mol Ecol (2003 May) PMID: 12694275
     Purugganan M, Gibson G
103. Molecular population genetics of the Arabidopsis CLAVATA2 region. The genomic scale of variation and selection in a selfing species.
     Genetics (2003 Mar) PMC1462473 free full-text archive
     Shepard KA, Purugganan MD
104. Selection on rapidly evolving proteins in the Arabidopsis genome.
     Genetics (2003 Feb) PMC1462452 free full-text archive
     Barrier M, Bustamante CD, Yu J, Purugganan MD
105. Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments.
     Genetics (2002 Dec) PMC1462365 free full-text archive
     Weinig C, Ungerer MC, Dorn LA, Kane NC, Toyonaga Y, Halldorsdottir SS, Mackay TF, Purugganan MD, Schmitt J
106. Molecular evidence on the origin and evolution of glutinous rice.
     Genetics (2002 Oct) PMC1462305 free full-text archive
     Olsen KM, Purugganan MD
107. GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): molecular evolution of growth regulators in a rapidly diversifying plant lineage.
     Mol Biol Evol (2002 Sep) PMID: 12200483
     Remington DL, Purugganan MD
108. Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway.
     Genetics (2002 Apr) PMC1462059 free full-text archive
     Olsen KM, Womack A, Garrett AR, Suddith JI, Purugganan MD
109. Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase.
     Mol Cell Biol (2002 May) PMC133788 free full-text archive
     Huye LE, Purugganan MM, Jiang MM, Roth DB
110. Distinct and opposite diversifying activities of terminal transferase splice variants.
     Nat Immunol (2002 May) PMID: 11938351
     Thai TH, Purugganan MM, Roth DB, Kearney JF
111. The cost of inbreeding in Arabidopsis.
     Nature (2002 Apr 4) PMID: 11932744
     Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL
112. Quantitative trait loci for inflorescence development in Arabidopsis thaliana.
     Genetics (2002 Mar) PMC1462026 free full-text archive
     Ungerer MC, Halldorsdottir SS, Modliszewski JL, Mackay TF, Purugganan MD
113. Map-based cloning of quantitative trait loci: progress and prospects.
     Genet Res (2001 Dec) PMID: 11865710
     Remington DL, Ungerer MC, Purugganan MD
114. The genetics of plant morphological evolution.
     Curr Opin Plant Biol (2002 Feb) PMID: 11788308
     Shepard KA, Purugganan MD
115. Accelerated regulatory gene evolution in an adaptive radiation.
     Proc Natl Acad Sci U S A (2001 Aug 28) PMC56940 free full-text archive
     Barrier M, Robichaux RH, Purugganan MD
116. Ku80 is required for addition of N nucleotides to V(D)J recombination junctions by terminal deoxynucleotidyl transferase.
     Nucleic Acids Res (2001 Apr 1) PMC31272 free full-text archive
     Purugganan MM, Shah S, Kearney JF, Roth DB
117. Quantitative trait loci for floral morphology in Arabidopsis thaliana.
     Genetics (2000 Nov) PMC1461322 free full-text archive
     Juenger T, Purugganan M, Mackay TF
118. The molecular population genetics of regulatory genes.
     Mol Ecol (2000 Oct) PMID: 11050541
     Purugganan MD
119. Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea.
     Genetics (2000 Jun) PMC1461124 free full-text archive
     Purugganan MD, Boyles AL, Suddith JI
120. Molecular evolution of flower development.
     Trends Ecol Evol (2000 Apr) PMID: 10717683
     Lawton‑Rauh AL, Alvarez‑Buylla ER, Purugganan MD
121. Interspecific evolution in plant microsatellite structure.
     Gene (2000 Jan 4) PMID: 10607903
     Barrier M, Friar E, Robichaux R, Purugganan M
122. Duplication of the Brassica oleracea APETALA1 floral homeotic gene and the evolution of domesticated cauliflower.
     J Hered (1999 Sep-Oct) PMID: 10544496
     Lowman AC, Purugganan MD
123. Patterns of molecular evolution among paralogous floral homeotic genes.
     Mol Biol Evol (1999 Aug) PMID: 10474900
     Lawton‑Rauh AL, Buckler ES 4th, Purugganan MD
124. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications.
     Mol Biol Evol (1999 Aug) PMID: 10474905
     Barrier M, Baldwin BG, Robichaux RH, Purugganan MD
125. Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana.
     Genetics (1999 Feb) PMC1460493 free full-text archive
     Purugganan MD, Suddith JI
126. The molecular evolution of development.
     Bioessays (1998 Sep) PMID: 9819559
     Purugganan MD
127. V(D)J recombination intermediates and non-standard products in XRCC4-deficient cells.
     Nucleic Acids Res (1998 Aug 15) PMC147771 free full-text archive
     Han JO, Erskine LA, Purugganan MM, Stamato TD, Roth DB
128. Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function.
     Proc Natl Acad Sci U S A (1998 Jul 7) PMC20941 free full-text archive
     Purugganan MD, Suddith JI
129. Cellular localization of Arabidopsis xyloglucan endotransglycosylase-related proteins during development and after wind stimulation.
     Plant Physiol (1997 Dec) PMC158597 free full-text archive
     Antosiewicz DM, Purugganan MM, Polisensky DH, Braam J
130. The Arabidopsis TCH4 xyloglucan endotransglycosylase. Substrate specificity, pH optimum, and cold tolerance.
     Plant Physiol (1997 Sep) PMC158473 free full-text archive
     Purugganan MM, Braam J, Fry SC
131. The evolution of the conserved ATPase domain (CAD): reconstructing the history of an ancient protein module.
     J Mol Evol (1997 Nov) PMID: 9342402
     Swaffield JC, Purugganan MD
132. The MADS-box floral homeotic gene lineages predate the origin of seed plants: phylogenetic and molecular clock estimates.
     J Mol Evol (1997 Oct) PMID: 9321418
     Purugganan MD
133. Plant responses to environmental stress: regulation and functions of the Arabidopsis TCH genes.
     Planta (1997) PMID: 9299794
     Braam J, Sistrunk ML, Polisensky DH, Xu W, Purugganan MM, Antosiewicz DM, Campbell P, Johnson KA
134. Life in a changing world: TCH gene regulation of expression and responses to environmental signals.
     Physiol Plant (1996 Dec) PMID: 11539337
     Braam J, Sistrunk ML, Polisensky DH, Xu W, Purugganan MM, Antosiewicz DM, Campbell P, Johnson KA
135. Evolution of development: molecules, mechanisms and phylogenetics.
     Trends Ecol Evol (1996) PMID: 21237741
     Purugganan MD
136. Arabidopsis TCH4, regulated by hormones and the environment, encodes a xyloglucan endotransglycosylase.
     Plant Cell (1995 Oct) PMC161010 free full-text archive
     Xu W, Purugganan MM, Polisensky DH, Antosiewicz DM, Fry SC, Braam J
137. Molecular evolution of flower development: diversification of the plant MADS-box regulatory gene family.
     Genetics (1995 May) PMC1206560 free full-text archive
     Purugganan MD, Rounsley SD, Schmidt RJ, Yanofsky MF
138. Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA.
     Mol Ecol (1995 Apr) PMID: 7735530
     Purugganan MD, Wessler SR
139. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon.
     Proc Natl Acad Sci U S A (1994 Nov 22) PMC45294 free full-text archive
     Purugganan MD, Wessler SR
140. Molecular evolution of the plant R regulatory gene family.
     Genetics (1994 Nov) PMC1206232 free full-text archive
     Purugganan MD, Wessler SR
141. Arabidopsis TCH3 encodes a novel Ca2+ binding protein and shows environmentally induced and tissue-specific regulation.
     Plant Cell (1994 Nov) PMC160543 free full-text archive
     Sistrunk ML, Antosiewicz DM, Purugganan MM, Braam J
142. Transposable elements as introns: evolutionary connections.
     Trends Ecol Evol (1993 Jul) PMID: 21236158
     Purugganan MD
143. Alternative splicing induced by insertion of retrotransposons into the maize waxy gene.
     Plant Cell (1992 Jul) PMC160176 free full-text archive
     Varagona MJ, Purugganan M, Wessler SR
144. The splicing of transposable elements and its role in intron evolution.
     Genetica (1992) PMID: 1334914
     Purugganan M, Wessler S
145. Filler DNA is associated with spontaneous deletions in maize.
     Proc Natl Acad Sci U S A (1990 Nov) PMC55033 free full-text archive
     Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R
146. The fractal nature of RNA secondary structure.
     Naturwissenschaften (1989 Oct) PMID: 2479842
     Purugganan MD
147. Accelerated electron transfer between metal complexes mediated by DNA.
     Science (1988 Sep 23) PMID: 3420416
     Purugganan MD, Kumar CV, Turro NJ, Barton JK