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Research Article

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

  • Jonathan A Eisen mail,

    To whom correspondence should be addressed. E-mail: jaeisen@ucdavis.edu

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤a Current address: University of California Davis Genome Center, Section of Evolution and Ecology, School of Biological Sciences and Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, California, United States of America

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  • Robert S Coyne,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Martin Wu,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Dongying Wu,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Mathangi Thiagarajan,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Jennifer R Wortman,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Jonathan H Badger,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Qinghu Ren,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Paolo Amedeo,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Kristie M Jones,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Luke J Tallon,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Arthur L Delcher,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤b Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

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  • Steven L Salzberg,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤b Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

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  • Joana C Silva,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • Brian J Haas,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

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  • William H Majoros,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤c Current address: Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America

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  • Maryam Farzad,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤d Current address: Agilent Technologies, Inc., Santa Clara, California, United States of America

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  • Jane M Carlton,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤e Current address: Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America

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  • Roger K Smith Jr.,

    Affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America

    ¤f Current address: Dupont Agriculture and Nutrition, Wilmington, Delaware, United States of America

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  • Jyoti Garg,

    Affiliation: Department of Biology, York University, Toronto, Ontario, Canada

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  • Ronald E Pearlman,

    Affiliations: Department of Biology, York University, Toronto, Ontario, Canada, Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada

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  • Kathleen M Karrer,

    Affiliation: Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America

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  • Lei Sun,

    Affiliation: Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America

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  • Gerard Manning,

    Affiliation: Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of America

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  • Nels C Elde,

    Affiliation: Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America

    ¤g Current address: Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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  • Aaron P Turkewitz,

    Affiliation: Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America

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  • David J Asai,

    Affiliation: Department of Biology, Harvey Mudd College, Claremont, California, United States of America

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  • David E Wilkes,

    Affiliation: Department of Biology, Harvey Mudd College, Claremont, California, United States of America

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  • Yufeng Wang,

    Affiliation: Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America

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  • Hong Cai,

    Affiliation: Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America

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  • Kathleen Collins,

    Affiliation: Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America

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  • B. Andrew Stewart,

    Affiliation: Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America

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  • Suzanne R Lee,

    Affiliation: Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America

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  • Katarzyna Wilamowska,

    Affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America

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  • Zasha Weinberg,

    Affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America

    ¤h Current address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America

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  • Walter L Ruzzo,

    Affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America

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  • Dorota Wloga,

    Affiliation: Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America

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  • Jacek Gaertig,

    Affiliation: Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America

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  • Joseph Frankel,

    Affiliation: Department of Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America

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  • Che-Chia Tsao,

    Affiliation: Department of Biology, University of Rochester, Rochester, New York, United States of America

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  • Martin A Gorovsky,

    Affiliation: Department of Biology, University of Rochester, Rochester, New York, United States of America

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  • Patrick J Keeling,

    Affiliation: Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

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  • Ross F Waller,

    Affiliation: Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

    ¤j Current address: School of Botany, The University of Melbourne, Melbourne, Australia

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  • Nicola J Patron,

    Affiliation: Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada

    ¤j Current address: School of Botany, The University of Melbourne, Melbourne, Australia

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  • J. Michael Cherry,

    Affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America

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  • Nicholas A Stover,

    Affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America

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  • Cynthia J Krieger,

    Affiliation: Department of Genetics, Stanford University, Stanford, California, United States of America

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  • Christina del Toro,

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

    ¤k Current address: Meharry Medical College, Nashville, Tennessee, United States of America

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  • Hilary F Ryder,

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

    ¤l Current address: Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, United States of America

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  • Sondra C Williamson,

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

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  • Rebecca A Barbeau,

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

    ¤m Current address: Lung Biology Center, University of California San Francisco, San Francisco, California, United States of America

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  • Eileen P Hamilton,

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

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  • Eduardo Orias

    Affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

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  • Published: August 29, 2006
  • DOI: 10.1371/journal.pbio.0040286

About the Authors

Jonathan A Eisen, Robert S Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R Wortman, Jonathan H Badger, Qinghu Ren, Paolo Amedeo, Kristie M Jones, Luke J Tallon, Arthur L Delcher, Steven L Salzberg, Joana C Silva, Brian J Haas, William H Majoros, Maryam Farzad, Jane M Carlton, Roger K Smith Jr.
The Institute for Genomic Research, Rockville, Maryland, United States of America
Jyoti Garg, Ronald E Pearlman
Department of Biology, York University, Toronto, Ontario, Canada
Ronald E Pearlman
Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
Kathleen M Karrer, Lei Sun
Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
Gerard Manning
Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of America
Nels C Elde, Aaron P Turkewitz
Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
David J Asai, David E Wilkes
Department of Biology, Harvey Mudd College, Claremont, California, United States of America
Yufeng Wang
Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America
Hong Cai
Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
Kathleen Collins, B. Andrew Stewart, Suzanne R Lee
Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
Katarzyna Wilamowska, Zasha Weinberg, Walter L Ruzzo
Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
Dorota Wloga, Jacek Gaertig
Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
Joseph Frankel
Department of Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America
Che-Chia Tsao, Martin A Gorovsky
Department of Biology, University of Rochester, Rochester, New York, United States of America
Patrick J Keeling, Ross F Waller, Nicola J Patron
Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
J. Michael Cherry, Nicholas A Stover, Cynthia J Krieger
Department of Genetics, Stanford University, Stanford, California, United States of America
Christina del Toro, Hilary F Ryder, Sondra C Williamson, Rebecca A Barbeau, Eileen P Hamilton, Eduardo Orias
Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America

Corresponding Author

Email: jaeisen@ucdavis.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

JAE coordinated the project. JAE, RSC, EPH, and EO wrote and edited the majority of the manuscript. JAE, RSC, MW, DW, JHB, and MT performed multiple bioinformatics analyses. MT, JRW, PA, MF, RKS, and BJH coordinated the annotation. KMJ and LJT carried out genome closure. ALD and SLS generated and analyzed genome assemblies. JCS, KMK, and LS analyzed mobile DNA elements. WHM generated gene models. QR conducted analyses of membrane transporters. JMC, JG, and REP generated and analyzed ESTs. GM analyzed protein kinases. NCE and APT analyzed membrane trafficking. DJA and DEW analyzed dyneins. YW and HC analyzed proteases. KC, BAS, SRL, WLR, KW, and ZW analyzed ncRNA. DW, JG, MAG, JF, and CCT analyzed cytoskeletal associated proteins. PJK, RFW, NJP, and JHB searched for plastid-derived genes. JMC, NAS, and CJK built TGD. CdT, HFR, SCW, and RAB performed the RAPD analyses. EPH, EO, SLS, JAE, and MW examined genome structure.