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Eichinger L, Pachebat J, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Babu MM, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail M, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox E, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. The genome of the social amoeba Dictyostelium discoideum. Nature 2005; 435:43-57. [PMID: 15875012 PMCID: PMC1352341 DOI: 10.1038/nature03481] [Citation(s) in RCA: 947] [Impact Index Per Article: 49.8] [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] [Received: 09/16/2004] [Accepted: 02/17/2005] [Indexed: 02/07/2023]
Abstract
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
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Affiliation(s)
- L. Eichinger
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - J.A. Pachebat
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - G. Glöckner
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M.-A. Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - M. Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - R. Olsen
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - K. Szafranski
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Q. Xu
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - B. Tunggal
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - S. Kummerfeld
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - M. Madera
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - B. A. Konfortov
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - F. Rivero
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - A. T. Bankier
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - R. Lehmann
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - N. Hamlin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Davies
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Gaudet
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - P. Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - K. Pilcher
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - G. Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Saunders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E. Sodergren
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - X. Nie
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Hall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Anjard
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - L. Hemphill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Bason
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Farbrother
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Desany
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - E. Just
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - T. Morio
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - R. Rost
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - C. Churcher
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Cooper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Haydock
- Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK
| | - N. van Driessche
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Cronin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - I. Goodhead
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - T. Mourier
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Pain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Harper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Lindsay
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - H. Hauser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. James
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Quiles
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Madan Babu
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - T. Saito
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810 Japan
| | - C. Buchrieser
- Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - A. Wardroper
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
- Department of Biology, University of York, York YO10 5YW, UK
| | - M. Felder
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M. Thangavelu
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
| | - D. Johnson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Knights
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Loulseged
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - K. Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. Oliver
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Price
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M.A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - J. Hernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - E. Rabbinowitsch
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Steffen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Sanders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Ma
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Y. Kohara
- Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - S. Sharp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Simmonds
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Spiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
| | - B. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Walker
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Woodward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - T. Winckler
- Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main, 60439, Germany
| | - Y. Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - G. Shaulsky
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - M. Schleicher
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - G. Weinstock
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Rosenthal
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - E.C. Cox
- Department of Molecular Biology, Princeton University, Princeton, NJ08544-1003, USA
| | - R. L. Chisholm
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - R. Gibbs
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W. F. Loomis
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M. Platzer
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - R. R. Kay
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - J. Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - P. H. Dear
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - A. A. Noegel
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Barrell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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