The cDNA Sequencing Project

  • Hideko Urushihara
  • Takahiro Morio
  • Yoshimasa Tanaka
Part of the Methods in Molecular Biology™ book series (MIMB, volume 346)


The Dictyostelium discoideum cDNA sequencing project started in 1995, preceding the genome sequencing project. Altogether, 14 cDNA libraries, including full-length ones, were constructed from five different stages of growth and asexual and sexual development, from which nearly 100,000 randomly chosen clones were sequenced to yield over 150,000 expressed sequence tags (ESTs). The data have been publicized online to facilitate clone distribution and collaboration using the whole clone set for microarray analyses. The EST reads were assembled to 6700 independent genes, which constitute about 55% of the total estimated Dictyostelium genes. Utilization of wet and dry resources have contributed to the understanding of the genetic system controlling the multicellular development in Dictyostelium.

Key Words

Dictyostelium discoideum development gene expression EST analysis DNA microarray in situ hybridization sequence database gene annotation promoter sequence 


  1. 1.
    Suzuki, Y., Yoshimoto-Nakagawa, K., Maruyama, K., Suyama, A. and Sugano, S. (1997) Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene 200, 149–156.PubMedCrossRefGoogle Scholar
  2. 2.
    Araki, T., Tsujioka, M., Abe, T., et al. (2003) A STAT-regulated, stress-induced signalling pathway in Dictyostelium. J. Cell Sci. 116, 2907–2915.PubMedCrossRefGoogle Scholar
  3. 3.
    Van Driessche, N., Shaw, C., Katoh, M., et al. (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129, 1543–1552.PubMedGoogle Scholar
  4. 4.
    Katoh, M., Shaw, C., Xu, Q., et al. (2004) An orderly retreat: Dedifferentiation is a regulated process. Proc. Natl. Acad. Sci. USA 101, 7005–7010.PubMedCrossRefGoogle Scholar
  5. 5.
    Maeda, M., Sakamoto, H., Iranfar, N., et al. (2003) Changing patterns of gene expression in prestalk cell subtypes of Dictyostelium recognized by in situ hybridization with genes from microarray analyses. Eukaryot. Cell 2, 627–637.PubMedCrossRefGoogle Scholar
  6. 6.
    Maruo, T., Sakamoto, H., Iranfar, N., et al. (2004) Control of cell type proportioning in Dictyostelium discoideum by Differentiation-Inducing Factor as determined by in situ hybridization. Eukaryot. Cell 3, 1241–1248.PubMedCrossRefGoogle Scholar
  7. 7.
    Farbrother, P., Wagner, C., Na, J., Tunggal, B., Morio, T., Urushihara, H., and Tanaka, Y. (2006) Dictyostelium transcriptional host cell response upon infection with Legionella. Cell Microbiol. 8, 438–456.PubMedCrossRefGoogle Scholar
  8. 8.
    Morio, T., Urushihara, H., Saito, T., et al. (1998) The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development. DNA Res. 5, 335–340.PubMedCrossRefGoogle Scholar
  9. 9.
    Urushihara, H., Morio, T., Saito, T., et al. (2004) Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum. Nucleic Acids Res. 32, 1647–1653.PubMedCrossRefGoogle Scholar
  10. 10.
    Eichinger, L., Pachebat, J. A., Glockner, G., et al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43–57.PubMedCrossRefGoogle Scholar
  11. 11.
    Muramoto, T., Suzuki, K., Shimizu, H., et al. (2003) Construction of a gamete-enriched gene pool and RNAi-mediated functional analysis in Dictyostelium discoideum. Mech. Dev. 120, 965–975.PubMedCrossRefGoogle Scholar
  12. 12.
    Bonner, J. T. (1947) Evidence for the formation of the aggregates by chemotaxis in the development of the slime mold Dictyostelium discoideum. J. Exp. Zool. 106, 1–26.PubMedCrossRefGoogle Scholar
  13. 13.
    Maruyama, K. and Sugano, S. (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171–174.PubMedCrossRefGoogle Scholar
  14. 14.
    Diatchenko, L., Lau, Y.-F. C., Campbell, A. P., et al. (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025–6030.PubMedCrossRefGoogle Scholar
  15. 15.
    Iranfar, N., Fuller, D., Sasik, R., Hwa, T., Laub, M., and Loomis, W. F. (2001) Expression patterns of cell-type-specific genes in Dictyostelium. Mol. Biol. Cell 12, 2590–2600.PubMedGoogle Scholar
  16. 16.
    Maruo, T., Sakamoto, H., Iranfar, N., et al. (2004) Control of cell type proportioning in Dictyostelium discoideum by differentiation-inducing factor as determined by in situ hybridization. Eukaryot. Cell 3, 1241–1248.PubMedCrossRefGoogle Scholar
  17. 17.
    Zhukovskaya, N. V., Fukuzawa, M., Tsujioka, M., et al. (2004) Dd-STATb, a Dictyostelium STAT protein with a highly aberrant SH2 domain, functions as a regulator of gene expression during growth and early development. Development 131, 447–458.PubMedCrossRefGoogle Scholar
  18. 18.
    Escalante, R., Iranfar, N., Sastre, L., and Loomis, W. F. (2004) Identification of genes dependent on the MADS box transcription factor SrfA in Dictyostelium discoideum development. Eukaryot. Cell 3, 564–566.PubMedCrossRefGoogle Scholar
  19. 19.
    Van Driessche, N., Demsar, J., Booth, E. O., et al. (2005) Epistasis analysis with global transcriptional phenotypes. Nat. Genet. 37, 471–477.PubMedCrossRefGoogle Scholar
  20. 20.
    Maeda, M., Kuwayama, H., Yokoyama, M., et al. (2000) Developmental changes in the spatial expression of genes involved in myosin function in Dictyostelium. Dev. Biol. 223, 114–119.PubMedCrossRefGoogle Scholar
  21. 21.
    Tsujioka, M., Yokoyama, M., Nishio, K., et al. (2001) Spatial expression patterns of genes involved in cyclic AMP responses in Dictyostelium discoideum development. Dev. Growth Differ. 43, 275–283.PubMedCrossRefGoogle Scholar
  22. 22.
    Thompson, C. R. and Kay, R. R. (2000) The role of DIF-1 signaling in Dictyostelium development. Mol. Cell 6, 1509–1514.PubMedCrossRefGoogle Scholar
  23. 23.
    Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202.PubMedGoogle Scholar
  24. 24.
    Yoshida, H., Kumimoto, H., and Okamoto, K. (1994) dutA RNA functions as an un-translatable RNA in the development of Dictyostelium discoideum. Nucleic Acids Res. 11, 41–46.CrossRefGoogle Scholar
  25. 25.
    Rivero, F. (2002) mRNA processing in Dictyostelium: sequence requirements for termination and splicing. Protist 153, 169–176.PubMedCrossRefGoogle Scholar
  26. 26.
    Suzuki, Y., Taira, H., Tsunoda, T., et al. (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2, 388–393.PubMedGoogle Scholar
  27. 27.
    Usuka, J., Zhu, W., and Brendel, V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16, 203–211.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2006

Authors and Affiliations

  • Hideko Urushihara
    • 1
  • Takahiro Morio
    • 1
  • Yoshimasa Tanaka
    • 1
  1. 1.Graduate School of Life and Environmental SciencesUniversity of TsukubaIbaraki-kenJapan

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