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Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernández E, Ferris P, Fukuzawa H, González-Ballester D, González-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riaño-Pachón DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martínez D, Ngau WCA, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007; 318:245-50. [PMID: 17932292 PMCID: PMC2875087 DOI: 10.1126/science.1143609] [Citation(s) in RCA: 1788] [Impact Index Per Article: 105.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
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Affiliation(s)
- Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Simon E. Prochnik
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Olivier Vallon
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | | | - Steven J. Karpowicz
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - George B. Witman
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Astrid Terry
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Asaf Salamov
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lillian K. Fritz-Laylin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
| | | | - Wallace F. Marshall
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Liang-Hu Qu
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - David R. Nelson
- Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics, University of Tennessee, Memphis, TN 38163, USA
| | - Anton A. Sanderfoot
- Department of Plant Biology, University of Minnesota, St. Paul MN 55108, USA
| | - Martin H. Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Qinghu Ren
- The Institute for Genomic Research, Rockville, MD 20850, USA
| | - Patrick Ferris
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Erika Lindquist
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Harris Shapiro
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Susan M. Lucas
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jane Grimwood
- Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Jeremy Schmutz
- Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Pierre Cardol
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
- Plant Biology Institute, Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Heriberto Cerutti
- University of Nebraska-Lincoln, School of Biological Sciences–Plant Science Initiative, Lincoln, NE 68588, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chun-Long Chen
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, CNRS, 67084 Strasbourg Cedex, France
| | - Martin T. Croft
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Rachel Dent
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Susan Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
| | - Patrick Ferris
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México 04510 DF, Mexico
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, D-33615 Bielefeld, Germany
| | - Marc Hanikenne
- Plant Biology Institute, Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Michael Hippler
- Department of Biology, Institute of Plant Biochemistry and Biotechnology, University of Münster, 48143 Münster, Germany
| | - William Inwood
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Kamel Jabbari
- CNRS UMR 8186, Département de Biologie, Ecole Normale Supérieure, 75230 Paris, France
| | - Ming Kalanon
- Plant Cell Biology Research Centre, The School of Botany, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Richard Kuras
- CNRS, UMR 7141, CNRS/Université Paris 6, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Paul A. Lefebvre
- Department of Plant Biology, University of Minnesota, St. Paul MN 55108, USA
| | - Stéphane D. Lemaire
- Institut de Biotechnologie des Plantes, UMR 8618, CNRS/Université Paris-Sud, Orsay, France
| | - Alexey V. Lobanov
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Martin Lohr
- Institut für Allgemeine Botanik, Johannes Gutenberg-Universität, 55099 Mainz, Germany
| | - Andrea Manuell
- Department of Cell Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Iris Meier
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Laurens Mets
- Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Maria Mittag
- Institut für Allgemeine Botanik und Pflanzenphysiologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Telsa Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - James V. Moroney
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Moseley
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
| | - Carolyn Napoli
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Aurora M. Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada E3B 6E1
| | - Krishna Niyogi
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Sergey V. Novoselov
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Ian T. Paulsen
- The Institute for Genomic Research, Rockville, MD 20850, USA
| | - Greg Pazour
- Department of Physiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Saul Purton
- Department of Biology, University College London, London WC1E 6BT, UK
| | - Jean-Philippe Ral
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS/USTL, IFR 118, Université des Sciences et Technologies de Lille, Cedex, France
| | | | - Wayne Riekhof
- Department of Medicine, National Jewish Medical and Research Center, Denver, CO 80206, USA
| | - Linda Rymarquis
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Michael Schroda
- Institute of Biology II/Plant Biochemistry, 79104 Freiburg, Germany
| | - David Stern
- Boyce Thompson Institute for Plant Research at Cornell University, Ithaca, NY 14853, USA
| | - James Umen
- Plant Biology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Robert Willows
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Nedra Wilson
- Department of Anatomy and Cell Biology, Oklahoma State University, Center for Health Sciences, Tulsa, OK 74107, USA
| | - Sara Lana Zimmer
- Boyce Thompson Institute for Plant Research at Cornell University, Ithaca, NY 14853, USA
| | - Jens Allmer
- Izmir Ekonomi Universitesi, 35330 Balcova-Izmir Turkey
| | - Janneke Balk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Katerina Bisova
- Institute of Microbiology, Czech Academy of Sciences, Czech Republic
| | - Chong-Jian Chen
- Biotechnology Research Center, Zhongshan University, Guangzhou 510275, China
| | - Marek Elias
- Department of Plant Physiology, Faculty of Sciences, Charles University, 128 44 Prague 2, Czech Republic
| | - Karla Gendler
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Charles Hauser
- Bioinformatics Program, St. Edward's University, Austin, TX 78704, USA
| | - Mary Rose Lamb
- Department of Biology, University of Puget Sound, Tacoma, WA 98407, USA
| | - Heidi Ledford
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Joanne C. Long
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jun Minagawa
- Institute of Low-Temperature Science, Hokkaido University, 060-0819, Japan
| | - M. Dudley Page
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Junmin Pan
- Department of Biology, Tsinghua University, Beijing, China 100084
| | - Wirulda Pootakham
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | | | - Eric Stahlberg
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Aimee M. Terauchi
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pinfen Yang
- Department of Biology, Marquette University, Milwaukee, WI 53233, USA
| | - Steven Ball
- UMR8576 CNRS, Laboratory of Biological Chemistry, 59655 Villeneuve d'Ascq, France
| | - Chris Bowler
- CNRS UMR 8186, Département de Biologie, Ecole Normale Supérieure, 75230 Paris, France
- Cell Signaling Laboratory, Stazione Zoologica, I 80121 Naples, Italy
| | - Carol L. Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Vadim N. Gladyshev
- Department of Biochemistry, N151 Beadle Center, University of Nebraska, Lincoln, NE 68588–0664, USA
| | - Pamela Green
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Richard Jorgensen
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Stephen Mayfield
- Department of Cell Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Sathish Rajamani
- Graduate Program in Biophysics, Ohio State University, Columbus, OH 43210, USA
| | - Richard T. Sayre
- PCMB and Plant Biotechnology Center, Ohio State University, Columbus, OH 43210, USA
| | - Peter Brokstein
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Inna Dubchak
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - David Goodstein
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Leila Hornick
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Y. Wayne Huang
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jinal Jhaveri
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yigong Luo
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Diego Martínez
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wing Chi Abby Ngau
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Bobby Otillar
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alexander Poliakov
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Aaron Porter
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lukasz Szajkowski
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gregory Werner
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Kemin Zhou
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Igor V. Grigoriev
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Daniel S. Rokhsar
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
| | - Arthur R. Grossman
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94306, USA
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