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.

1. Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
2. Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
3. Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
4. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
5. Verna and Marrs McLean Department of Biochemistry and Molecular Biology,
6. Department of Molecular and Human Genetics,
7. Graduate Program in Structural and Computational Biology and Molecular Biophysics, and
8. Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
9. Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, California 92093, USA
10. dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, Illinois 60611, USA
11. Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
12. Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
13. Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK
14. Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
15. Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
16. Department of Biology, University of York, York YO10 5YW, UK
17. MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
18. Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
19. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
20. Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main 60439, Germany
21. Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1003, USA
22. School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
23. *These authors contributed equally to this work
24. †Present address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA

Correspondence to: P. H. Dear² Correspondence and requests for materials should be addressed to P.H.D. (Email: phd@mrc-lmb.cam.ac.uk). Sequence data for the genome were deposited in the GenBank nucleotide database under the project accession number AAFI00000000. The six chromosomal assemblies have accession numbers CM000150−CM000155, and their component sequence contigs have accession numbers AAFI01000001−AAFI01000336.

Received 16 September 2004; Accepted 17 February 2005

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