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.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Goffeau, A. et al. Life with 6000 genes. Science 274, 546–567 (1996)
Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002)
The C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998)
Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000)
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000)
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977 (2000)
Loomis, W. F. Genetic networks that regulate development in Dictyostelium cells. Microbiol. Rev. 60, 135–150 (1996)
Eichinger, L., Lee, S. S. & Schleicher, M. Dictyostelium as model system for studies of the actin cytoskeleton by molecular genetics. Microsc. Res. Technol. 47, 124–134 (1999)
Parent, C. A. & Devreotes, P. N. A cell's sense of direction. Science 284, 765–770 (1999)
Firtel, R. A. & Meili, R. Dictyostelium: a model for regulated cell movement during morphogenesis. Curr. Opin. Genet. Dev. 10, 421–427 (2000)
Noegel, A. A. & Schleicher, M. The actin cytoskeleton of Dictyostelium: a story told by mutants. J. Cell Sci. 113, 759–766 (2000)
Kay, R. R. & Williams, J. G. The Dictyostelium genome project: an invitation to species hopping. Trends Genet. 15, 294–297 (1999)
Cox, E. C., Vocke, C. D., Walter, S., Gregg, K. Y. & Bain, E. S. Electrophoretic karyotype for Dictyostelium discoideum. Proc. Natl Acad. Sci. USA 87, 8247–8251 (1990)
Loomis, W. F. & Kuspa, A. Dictyostelium—A Model System for Cell and Developmental Biology (eds Maeda, Y., Inouye, K. & Takeuchi, I.) 15–30 (Universal Academic, Tokyo, 1997)
Gardner, M. J. et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132 (1998)
Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532–538 (1999)
Glöckner, G. Large scale sequencing and analysis of AT rich eukaryote genomes. Curr. Genom. 1, 289–299 (2000)
Glöckner, G. et al. The complex repeats of Dictyostelium discoideum. Genome Res. 11, 585–594 (2001)
Dear, P. H. in Genome Mapping—A Practical Approach (ed. Dear, P. H.) 95–124 (IRL Press, Oxford, 1997)
Pan, W. C. & Blackburn, E. H. Single extrachromosomal ribosomal RNA gene copies are synthesized during amplification of the rDNA in Tetrahymena. Cell 23, 459–466 (1981)
Lim, L. P. & Burge, C. B. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA 98, 11193–11198 (2001)
Morio, T. et al. The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development. DNA Res. 5, 335–340 (1998)
Apweiler, R. et al. InterPro—an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16, 1145–1150 (2000)
Goebl, M. G. & Petes, T. D. Most of the yeast genomic sequences are not essential for cell growth and division. Cell 46, 983–992 (1986)
Konfortov, B. A., Cohen, H. M., Bankier, A. T. & Dear, P. H. A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6. Genome Res. 10, 1737–1742 (2000)
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997)
Parra, G., Blanco, E. & Guigo, R. GeneID in Drosophila. Genome Res. 10, 511–515 (2000)
The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)
Fortini, M. E., Skupski, M. P., Boguski, M. S. & Hariharan, I. K. A survey of human disease gene counterparts in the Drosophila genome. J. Cell Biol. 150, F23–F30 (2000)
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.
The authors declare that they have no competing financial interests.
About this article
Reaumuria trigyna transcription factor RtWRKY23 enhances salt stress tolerance and delays flowering in plants
Journal of Plant Physiology (2019)
International Journal of Molecular Sciences (2018)
Current Protocols in Bioinformatics (2018)
Scientific Reports (2017)
BMC Cell Biology (2017)