Sequence and analysis of chromosome 2 of Dictyostelium discoideum

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Abstract

The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene density, about 1 gene per 2.6 kilobases (kb), is surpassed only by Saccharomyces cerevisiae (one per 2 kb) and is similar to that of Schizosaccharomyces pombe (one per 2.5 kb)1,2. If we assume that the other chromosomes have a similar gene density, we can expect around 11,000 genes in the D. discoideum genome. A significant number of the genes show higher similarities to genes of vertebrates than to those of other fully sequenced eukaryotes1,2,3,4,5,6. This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom7, placing it close to the base of metazoan evolution.

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Figure 1: Feature distribution on chromosome 2.
Figure 2: Functional classification of D. discoideum chromosome 2-coded proteins.
Figure 3: Phylum-specific distribution of proteins.

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Acknowledgements

We thank S. Förste, N. Zeisse, S. Rothe, S. Landmann, R. Schultz, S. Müller and R. Müller for expert technical assistance. We also thank the working team of the Japanese cDNA project (http://www.csm.biol.tsukuba.ac.jp/cDNAproject.html) for sharing data. The sequencing of chromosome 2 was supported by the Deutsche Forschungsgemeinschaft, with partial support by Köln Fortune. Additional support was obtained from the NIH, the Medical Research Council and the EU. Members of the Sanger Institute Dictyostelium discoideum sequencing team are listed at http://www.sanger.ac.uk/Projects/D_discoideum/team.shtml.

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Correspondence to Gernot Glöckner or Ludwig Eichinger or Angelika A. Noegel.

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The authors declare that they have no competing financial interests.

Supplementary information

Index to genome project, links to imags and tables and external web data (HTM 7 kb)

Splice site characteristics (HTM 2 kb)

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