The genome of the social amoeba Dictyostelium discoideum

• Published in: Nature Vol. 435; no. 7038; pp. 43 - 57
• Main Authors: Dear, P. H, Eichinger, L, Pachebat, J. A, Glöckner, G, Rajandream, M.-A, Sucgang, R, Berriman, M, Song, J, Olsen, R, Szafranski, K, Xu, Q, Tunggal, B, Kummerfeld, S, Madera, M, Konfortov, B. A, Rivero, F, Bankier, A. T, 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, Madan Babu, M, Saito, T, Buchrieser, C, Wardroper, A, Felder, M, Thangavelu, M, Johnson, D, Knights, A, Loulseged, H, Mungall, K, Oliver, K, Price, C, Quail, M. A, 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. C, Chisholm, R. L, Gibbs, R, Loomis, W. F, Platzer, M, Kay, R. R, Williams, J, Noegel, A. A, Barrell, B, Kuspa, A
• Format: Journal Article
• Language: English
• Published: London Nature Publishing 05.05.2005; Nature Publishing Group
• Subjects: Amino acids; Amoeba; Animals; ATP-Binding Cassette Transporters - genetics; Base Composition; Biological and medical sciences; Cell Adhesion - genetics; Cell Movement - genetics; Centromere - genetics; Chromosomes; Conserved Sequence - genetics; Dictyostelium - cytology; Dictyostelium - enzymology; Dictyostelium - genetics; Dictyostelium - metabolism; Dictyostelium discoideum; DNA Transposable Elements - genetics; DNA, Ribosomal - genetics; Eukaryotic Cells - metabolism; Fundamental and applied biological sciences. Psychology; Gene Duplication; Gene Transfer, Horizontal - genetics; Genes. Genome; Genetic diversity; Genome; Genomics; Humans; Microorganisms; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Phylogeny; Proteins; Proteome; Protozoan Proteins - chemistry; Protozoan Proteins - genetics; Repetitive Sequences, Nucleic Acid - genetics; RNA, Transfer - genetics; Sequence Analysis, DNA; Signal Transduction - genetics; Social Behavior; Telomere - genetics; Dictyostelium discoideum; Protozoa; Extrachromosomal DNA; Gene; Ribosomal DNA; Chromosome; Genome; Protein; Mycetozoa
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature03481

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.