The genome of the social amoeba Dictyostelium discoideum
L. Eichinger,1† J.A. Pachebat,2,1† G. Glöckner,3† M.-A. Rajandream,4† R. Sucgang,5† M. Berriman,4 J. Song,5 R. Olsen,6 K. Szafranski,3 Q. Xu,7,8 B. Tunggal,1 S. Kummerfeld,2 M. Madera,2 B. A. Konfortov,2 F. Rivero,1 A. T. Bankier,2 R. Lehmann,3 N. Hamlin,4 R. Davies,4 P. Gaudet,9 P. Fey,9 K. Pilcher,9 G. Chen,5 D. Saunders,4 E. Sodergren,7,10 P. Davis,4 A. Kerhornou,4 X. Nie,5 N. Hall,4a C. Anjard,6 L. Hemphill,5 N. Bason,4 P. Farbrother,1 B. Desany,5 E. Just,9 T. Morio,11 R. Rost,12 C. Churcher,4 J. Cooper,4 S. Haydock,13 N. van Driessche,7 A. Cronin,4 I. Goodhead,4 D. Muzny,10 T. Mourier,4 A. Pain,4 M. Lu,5 D. Harper,4 R. Lindsay,5 H. Hauser,4 K. James,4 M. Quiles,10 M. Madan Babu,2 T. Saito,14 C. Buchrieser,15 A. Wardroper,16,2 M. Felder,3 M. Thangavelu,17 D. Johnson,4 A. Knights,4 H. Loulseged,10 K. Mungall,4 K. Oliver,4 C. Price,4 M.A. Quail,4 H. Urushihara,11 J. Hernandez,10 E. Rabbinowitsch,4 D. Steffen,10 M. Sanders,4 J. Ma,10 Y. Kohara,18 S. Sharp,4 M. Simmonds,4 S. Spiegler,4 A. Tivey,4 S. Sugano,19 B. White,4 D. Walker,4 J. Woodward,4 T. Winckler,20 Y. Tanaka,11 G. Shaulsky,7,8 M. Schleicher,12 G. Weinstock,7,10 A. Rosenthal,3 E.C. Cox,21 R. L. Chisholm,9 R. Gibbs,7,10 W. F. Loomis,6 M. Platzer,3‡ R. R. Kay,2‡ J. Williams,22‡ P. H. Dear,2‡§ A. A. Noegel,1‡ B. Barrell,4‡ and A. Kuspa5,7‡
1Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
2Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
3Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
4The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
5Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
6Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
7Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
8Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
9dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
10Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
11Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
12Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
13Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK.
14Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810 Japan
15Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
16Department of Biology, University of York, York YO10 5YW, UK.
17MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK.
18Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
19Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
20Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main, 60439, Germany
21Department of Molecular Biology, Princeton University, Princeton, NJ08544-1003, USA
22School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
§Corresponding author., Telephone:  1223 402190, Fax:  1223 412178, Email:[email protected]
aPresent address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, USA
†These authors contributed equally.
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 encode ~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 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 appears to have retained more of the diversity of the ancestral genome than either of these two groups.
Nature. 2005 May 5; 435(7038): 43–57.
The amoebozoa are a richly diverse group of organisms whose genomes remain largely unexplored. The soil-dwelling social amoeba Dictyostelium discoideum
has been actively studied for the past fifty years and has contributed greatly to our understanding of cellular motility, signalling and interaction1
. For example, studies in Dictyostelium
provided the first descriptions of a eukaryotic cell chemo-attractant and a cell-cell adhesion protein2, 3
Dictyostelium amoebae inhabit forest soil consuming bacteria and yeast, which they track by chemotaxis. Starvation, however, prompts the solitary cells to aggregate and to develop as a true multicellular organism, producing a fruiting body comprised of a cellular, cellulosic stalk supporting a bolus of spores. Thus, Dictyostelium has evolved mechanisms that direct the differentiation of a homogeneous population of cells into distinct cell types, regulate the proportions between tissues and orchestrate the construction of an effective structure for the dispersal of spores4. Many of the genes necessary for these processes in Dictyostelium were also inherited by metazoa and fashioned through evolution for use within many different modes of development.
The amoebozoa are also noteworthy as representing one of the earliest branches from the last common ancestor of all eukaryotes. Each of the surviving branches of the crown group of eukaryotes provides an example of the ways in which the ancestral genome has been sculpted and adapted by lineage-specific gene duplication, divergence and deletion. Comparison between representatives of these branches promises to shed light not only on the nature and content of the ancestral eukaryotic genome, but on the diversity of ways in which its components have been adapted to meet the needs of complex organisms. The genome of Dictyostelium, as the first free-living protozoan to be fully sequenced, should be particularly informative for these analyses.