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Michael Purugganan

Silver Professor; Professor of Biology; Co-Principal Investigator

    1988 …2020

    Research output per year

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    Research Output

    2020

    An inferred fitness consequence map of the rice genome

    Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A. & Purugganan, M. D., Feb 1 2020, In : Nature Plants. 6, 2, p. 119-130 12 p.

    Research output: Contribution to journalArticle

    Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

    Choi, J. Y., Purugganan, M. & Stacy, E. A., Mar 1 2020, In : Molecular Biology and Evolution. 37, 3, p. 695-710 16 p.

    Research output: Contribution to journalArticle

    Open Access

    Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

    Read, A. C., Moscou, M. J., Zimin, A. V., Pertea, G., Meyer, R. S., Purugganan, M. D., Leach, J. E., Triplett, L. R., Salzberg, S. L. & Bogdanove, A. J., Jan 1 2020, In : PLoS genetics. 16, 1, e1008571.

    Research output: Contribution to journalArticle

    Open Access

    Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

    Choi, J. Y., Lye, Z. N., Groen, S. C., Dai, X., Rughani, P., Zaaijer, S., Harrington, E. D., Juul, S. & Purugganan, M. D., Feb 5 2020, In : Genome biology. 21, 1, 21.

    Research output: Contribution to journalArticle

    Open Access

    The strength and pattern of natural selection on gene expression in rice

    Groen, S. C., Ćalić, I., Joly-Lopez, Z., Platts, A. E., Choi, J. Y., Natividad, M., Dorph, K., Mauck, W. M., Bracken, B., Cabral, C. L. U., Kumar, A., Torres, R. O., Satija, R., Vergara, G., Henry, A., Franks, S. J. & Purugganan, M. D., Feb 27 2020, In : Nature. 578, 7796, p. 572-576 5 p.

    Research output: Contribution to journalArticle

    2019

    Copy Number Variation in Domestication

    Lye, Z. N. & Purugganan, M. D., Apr 2019, In : Trends in Plant Science. 24, 4, p. 352-365 14 p.

    Research output: Contribution to journalReview article

    Cross-species hybridization and the origin of North African date palms

    Flowers, J. M., Hazzouri, K. M., Gros-Balthazard, M., Mo, Z., Koutroumpa, K., Perrakis, A., Ferrand, S., Khierallah, H. S. M., Fuller, D. Q., Aberlenc, F., Fournaraki, C. & Purugganan, M. D., Jan 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 5, p. 1651-1658 8 p.

    Research output: Contribution to journalArticle

    Evolutionary and ecological functional genomics, from lab to the wild

    Zaidem, M. L., Groen, S. C. & Purugganan, M. D., Jan 2019, In : Plant Journal. 97, 1, p. 40-55 16 p.

    Research output: Contribution to journalArticle

    Evolutionary Insights into the Nature of Plant Domestication

    Purugganan, M. D., Jul 22 2019, In : Current Biology. 29, 14, p. R705-R714

    Research output: Contribution to journalReview article

    Open Access

    Genome-wide association mapping of date palm fruit traits

    Hazzouri, K. M., Gros-Balthazard, M., Flowers, J. M., Copetti, D., Lemansour, A., Lebrun, M., Masmoudi, K., Ferrand, S., Dhar, M. I., Fresquez, Z. A., Rosas, U., Zhang, J., Talag, J., Lee, S., Kudrna, D., Powell, R. F., Leitch, I. J., Krueger, R. R., Wing, R. A., Amiri, K. M. A. & 1 others, Purugganan, M. D., Dec 1 2019, In : Nature communications. 10, 1, 4680.

    Research output: Contribution to journalArticle

    Open Access

    The bracteatus pineapple genome and domestication of clonally propagated crops

    Chen, L. Y., VanBuren, R., Paris, M., Zhou, H., Zhang, X., Wai, C. M., 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, T. Y. & 25 others, Kao, S. M., Choi, J. Y., Sharma, A., Song, J., Wang, L., Yim, W. C., Cushman, J. C., Paull, R. E., Matsumoto, T., Qin, Y., Wu, Q., Wang, J., Yu, Q., Wu, J., Zhang, S., Boches, P., Tung, C. W., Wang, M. L., Coppens d’Eeckenbrugge, G., Sanewski, G. M., Purugganan, M. D., Schatz, M. C., Bennetzen, J. L., Lexer, C. & Ming, R., Oct 1 2019, In : Nature Genetics. 51, 10, p. 1549-1558 10 p.

    Research output: Contribution to journalArticle

    Open Access

    The complex geography of domestication of the African rice oryza glaberrima

    Choi, J. Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R. K. & Purugganan, M. D., Mar 2019, In : PLoS genetics. 15, 3, e1007414.

    Research output: Contribution to journalArticle

    Open Access

    Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

    Dreissig, S., Mascher, M., Heckmann, S. & Purugganan, M., Sep 1 2019, In : Molecular Biology and Evolution. 36, 9, p. 2029-2039 11 p.

    Research output: Contribution to journalArticle

    Open Access
    2018

    Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

    Choi, J. Y. & Purugganan, M. D., Feb 2018, In : Molecular Biology and Evolution. 35, 2, p. 365-382 18 p.

    Research output: Contribution to journalArticle

    Mapping of HKT1;5 gene in barley using gwas approach and its implication in salt tolerance mechanism

    Hazzouri, K. M., Khraiwesh, B., Amiri, K. M. A., Pauli, D., Blake, T., Shahid, M., Mullath, S. K., Nelson, D., Mansour, A. L., Salehi-Ashtiani, K., Purugganan, M. & Masmoudi, K., Feb 19 2018, In : Frontiers in Plant Science. 9, 156.

    Research output: Contribution to journalArticle

    Multiple origin but single domestication led to Oryza sativa

    Choi, J. Y. & Purugganan, M. D., Mar 1 2018, In : G3: Genes, Genomes, Genetics. 8, 3, p. 797-803 7 p.

    Research output: Contribution to journalArticle

    The rice genome revolution: From an ancient grain to Green Super Rice

    Wing, R. A., Purugganan, M. D. & Zhang, Q., Aug 1 2018, In : Nature Reviews Genetics. 19, 8, p. 505-517 13 p.

    Research output: Contribution to journalReview article

    2017

    Seed plant-specific gene lineages involved in carpel development

    Pfannebecker, K. C., Lange, M., Rupp, O., Becker, A. & Purugganan, M., Apr 1 2017, In : Molecular Biology and Evolution. 34, 4, p. 925-942 18 p.

    Research output: Contribution to journalArticle

    The rice paradox: Multiple origins but single domestication in Asian Rice

    Choi, J. Y., Platts, A. E., Fuller, D. Q., Hsing, Y. I., Wing, R. A., Purugganan, M. D. & Kim, Y., Apr 1 2017, In : Molecular Biology and Evolution. 34, 4, p. 969-979 11 p.

    Research output: Contribution to journalArticle

    2016

    Cryptic genetic variation for arabidopsis thaliana seed germination speed in a novel salt stress environment

    Yuan, W., Flowers, J. M., Sahraie, D. J. & Purugganan, M. D., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 10, p. 3129-3138 10 p.

    Research output: Contribution to journalArticle

    Developing maps of fitness consequences for plant genomes

    Joly-Lopez, Z., Flowers, J. M. & Purugganan, M. D., Apr 1 2016, In : Current Opinion in Plant Biology. 30, p. 101-107 7 p.

    Research output: Contribution to journalReview article

    Domestication history and geographical adaptation inferred from a SNP map of African rice

    Meyer, R. S., Choi, J. Y., Sanches, M., Plessis, A., Flowers, J. M., Amas, J., Dorph, K., Barretto, A., Gross, B., Fuller, D. Q., Bimpong, I. K., Ndjiondjop, M. N., Hazzouri, K. M., Gregorio, G. B. & Purugganan, M. D., Sep 1 2016, In : Nature Genetics. 48, 9, p. 1083-1088 6 p.

    Research output: Contribution to journalArticle

    EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments

    Wilkins, O., Hafemeister, C., Plessis, A., Holloway-Phillips, M. M., Pham, G. M., Nicotra, A. B., Gregorio, G. B., Krishna Jagadish, S. V., Septiningsih, E. M., Bonneau, R. & Purugganan, M., Oct 2016, In : Plant Cell. 28, 10, p. 2365-2384 20 p.

    Research output: Contribution to journalArticle

    Evolution of plant phenotypes, from genomes to traits

    Casacuberta, J. M., Jackson, S., Panaud, O., Purugganan, M. & Wendel, J., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 4, p. 775-778 4 p.

    Research output: Contribution to journalComment/debate

    Extreme QTL mapping of germination speed in Arabidopsis thaliana

    Yuan, W., Flowers, J. M., Sahraie, D. J., Ehrenreich, I. M. & Purugganan, M. D., Sep 1 2016, In : Molecular ecology. 25, 17, p. 4177-4196 20 p.

    Research output: Contribution to journalArticle

    Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis

    Rest, J. S., Wilkins, O., Yuan, W., Purugganan, M. D. & Gurevitch, J., Feb 1 2016, In : Plant Journal. 85, 4, p. 548-560 13 p.

    Research output: Contribution to journalArticle

    Systems genetics of plant adaptation to environmental stresses

    Groen, S. C. & Purugganan, M. D., Jan 1 2016, In : Applications in Plant Sciences. 103, 12, p. 2019-2021 3 p.

    Research output: Contribution to journalComment/debate

    Tracing ancestor rice of Suriname Maroons back to its African origin

    Van Andel, T. R., Meyer, R. S., Aflitos, S. A., Carney, J. A., Veltman, M. A., Copetti, D., Flowers, J. M., Havinga, R. M., Maat, H., Purugganan, M. D., Wing, R. A. & Schranz, M. E., Oct 3 2016, In : Nature Plants. 2, 16149.

    Research output: Contribution to journalLetter

    2015

    Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

    Pires, I. S., Negrão, S., Oliveira, M. M. & Purugganan, M. D., Sep 1 2015, In : Physiologia Plantarum. 155, 1, p. 43-54 12 p.

    Research output: Contribution to journalArticle

    Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

    Plessis, A., Hafemeister, C., Wilkins, O., Gonzaga, Z. J., Meyer, R. S., Pires, I., Müller, C., Septiningsih, E. M., Bonneau, R. & Purugganan, M., Nov 26 2015, In : eLife. 4, NOVEMBER2015, e08411.

    Research output: Contribution to journalArticle

    Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

    Hazzouri, K. M., Flowers, J. M., Visser, H. J., Khierallah, H. S. M., Rosas, U., Pham, G. M., Meyer, R. S., Johansen, C. K., Fresquez, Z. A., Masmoudi, K., Haider, N., El Kadri, N., Idaghdour, Y., Malek, J. A., Thirkhill, D., Markhand, G. S., Krueger, R. R., Zaid, A. & Purugganan, M. D., Nov 9 2015, In : Nature communications. 6, 8824.

    Research output: Contribution to journalArticle

    Whole-genome resequencing reveals extensive natural variation in the model green alga chlamydomonas reinhardtii

    Flowers, J. M., Hazzouri, K. M., Pham, G. M., Rosas, U., Bahmani, T., Khraiwesh, B., Nelson, D. R., Jijakli, K., Abdrabu, R., Harris, E. H., Lefebvre, P. A., Hom, E. F. Y., Salehi-Ashtiani, K. & Purugganan, M. D., Jan 1 2015, In : Plant Cell. 27, 9, p. 2353-2369 17 p.

    Research output: Contribution to journalArticle

    2014

    An evolutionary genomic tale of two rice species

    Purugganan, M. D., Jan 1 2014, In : Nature Genetics. 46, 9, p. 931-932 2 p.

    Research output: Contribution to journalShort survey

    Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

    Fuller, D. Q., Denham, T., Arroyo-Kalin, M., Lucas, L., Stevens, C. J., Qin, L., Allaby, R. G. & Purugganan, M. D., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6147-6152 6 p.

    Research output: Contribution to journalArticle

    Current perspectives and the future of domestication studies

    Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo-Kalin, M., Barton, L., Vigueira, C. C., Denham, T., Dobney, K., Doust, A. N., Gepts, P., Gilbert, M. T. P., Gremillion, K. J., Lucas, L., Lukens, L., Marshall, F. B., Olsen, K. M., Pires, J. C., Richerson, P. J. & 4 others, De Casas, R. R., Sanjur, O. I., Thomas, M. G. & Fuller, D. Q., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6139-6146 8 p.

    Research output: Contribution to journalReview article

    Population Genomics of Plant Species

    Hazzouri, K. M., Purugganan, M. D. & Flowers, J. M., 2014, Advances in Botanical Research. Academic Press Inc., p. 311-334 24 p. (Advances in Botanical Research; vol. 69).

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

    Molina, J., Hazzouri, K. M., Nickrent, D., Geisler, M., Meyer, R. S., Pentony, M. M., Flowers, J. M., Pelser, P., Barcelona, J., Inovejas, S. A., Uy, I., Yuan, W., Wilkins, O., Michel, C. I., Locklear, S., Concepcion, G. P. & Purugganan, M. D., Apr 1 2014, In : Molecular Biology and Evolution. 31, 4, p. 793-803 11 p.

    Research output: Contribution to journalArticle

    Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum

    Li, S. I., Buttery, N. J., Thompson, C. R. L. & Purugganan, M. D., Jul 21 2014, In : BMC Genomics. 15, 1, 616.

    Research output: Contribution to journalArticle

    Storytelling and story testing in domestication

    Gerbault, P., Allaby, R. G., Boivin, N., Rudzinski, A., Grimaldi, I. M., Pires, J. C., Climer Vigueira, C., Dobney, K., Gremillion, K. J., Barton, L., Arroyo-Kalin, M., Purugganan, M. D., De Casas, R. R., Bollongino, R., Burger, J., Fuller, D. Q., Bradley, D. G., Balding, D. J., Richerson, P. J., Gilbert, M. T. P. & 2 others, Larson, G. & Thomas, M. G., Apr 29 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 17, p. 6159-6164 6 p.

    Research output: Contribution to journalArticle

    Variation in arabidopsis flowering time associated with cis-regulatory variation in CONSTANS

    Rosas, U., Mei, Y., Xie, Q., Banta, J. A., Zhou, R. W., Seufferheld, G., Gerard, S., Chou, L., Bhambhra, N., Parks, J. D., Flowers, J. M., McClung, C. R., Hanzawa, Y. & Purugganan, M. D., Apr 16 2014, In : Nature communications. 5, 3651.

    Research output: Contribution to journalArticle

    2013

    Different evolutionary histories of two cation/proton exchanger gene families in plants

    Pires, I. S., Negrão, S., Pentony, M. M., Abreu, I. A., Oliveira, M. M. & Purugganan, M. D., Jul 4 2013, In : BMC Plant Biology. 13, 1, 97.

    Research output: Contribution to journalArticle

    Evolution of crop species: Genetics of domestication and diversification

    Meyer, R. S. & Purugganan, M. D., Dec 1 2013, In : Nature Reviews Genetics. 14, 12, p. 840-852 13 p.

    Research output: Contribution to journalReview article

    Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture

    Rosas, U., Cibrian-Jaramillo, A., Ristova, D., Banta, J. A., Gifford, M. L., Fan, A. H., Zhou, R. W., Kim, G. J., Krouk, G., Birnbaum, K. D., Purugganan, M. D. & Coruzzi, G. M., Sep 10 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 37, p. 15133-15138 6 p.

    Research output: Contribution to journalArticle

    Introduction to theme "genomics in ecology, evolution, and systematics"

    Shaffer, H. B. & Purugganan, M. D., Nov 2013, In : Annual Review of Ecology, Evolution, and Systematics. 44, p. 1-4 4 p.

    Research output: Contribution to journalReview article

    Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

    Li, Y. H., Zhao, S. C., Ma, J. X., Li, D., Yan, L., Li, J., Qi, X. T., Guo, X. S., Zhang, L., He, W. M., Chang, R. Z., Liang, Q. S., Guo, Y., Ye, C., Wang, X. B., Tao, Y., Guan, R. X., Wang, J. Y., Liu, Y. L., Jin, L. G. & 15 others, Zhang, X. Q., Liu, Z. X., Zhang, L. J., Chen, J., Wang, K. J., Nielsen, R., Li, R. Q., Chen, P. Y., Li, W. B., Reif, J. C., Purugganan, M., Wang, J., Zhang, M. C., Wang, J. & Qiu, L. J., Aug 28 2013, In : BMC Genomics. 14, 1, 579.

    Research output: Contribution to journalArticle

    Molecular relationships between australian annual wild rice, Oryza meridionalis, and two related perennial forms

    Sotowa, M., Ootsuka, K., Kobayashi, Y., Hao, Y., Tanaka, K., Ichitani, K., Flowers, J. M., Purugganan, M. D., Nakamura, I., Sato, Y. I., Sato, T., Crayn, D., Simon, B., Waters, D. L. E., Henry, R. J. & Ishikawa, R., Jan 1 2013, In : Rice. 6, 26

    Research output: Contribution to journalArticle

    Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

    Gifford, M. L., Banta, J. A., Katari, M. S., Hulsmans, J., Chen, L., Ristova, D., Tranchina, D., Purugganan, M. D., Coruzzi, G. M. & Birnbaum, K. D., Sep 1 2013, In : PLoS genetics. 9, 9, e1003760.

    Research output: Contribution to journalArticle

    Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the drosophila retina

    Thanawala, S. U., Rister, J., Goldberg, G. W., Zuskov, A., Olesnicky, E. C., Flowers, J. M., Jukam, D., Purugganan, M. D., Gavis, E. R., Desplan, C. & Johnston, R. J., Apr 15 2013, In : Developmental Cell. 25, 1, p. 93-105 13 p.

    Research output: Contribution to journalArticle

    2012

    Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana

    Banta, J. A., Ehrenreich, I. M., Gerard, S., Chou, L., Wilczek, A., Schmitt, J., Kover, P. X. & Purugganan, M. D., Aug 1 2012, In : Ecology Letters. 15, 8, p. 769-777 9 p.

    Research output: Contribution to journalArticle