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Science 24 March 2000:
Vol. 287. no. 5461, pp. 2204 - 2215
DOI: 10.1126/science.287.5461.2204
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Review

Comparative Genomics of the Eukaryotes

Gerald M. Rubin, 1 Mark D. Yandell, 3 Jennifer R. Wortman, 3 George L. Gabor Miklos, 4 Catherine R. Nelson, 2 Iswar K. Hariharan, 5 Mark E. Fortini, 6 Peter W. Li, 3 Rolf Apweiler, 7 Wolfgang Fleischmann, 7 J. Michael Cherry, 8 Steven Henikoff, 9 Marian P. Skupski, 3 Sima Misra, 2 Michael Ashburner, 7 Ewan Birney, 7 Mark S. Boguski, 10 Thomas Brody, 11 Peter Brokstein, 2 Susan E. Celniker, 12 Stephen A. Chervitz, 13 David Coates, 14 Anibal Cravchik, 3 Andrei Gabrielian, 3 Richard F. Galle, 12 William M. Gelbart, 15 Reed A. George, 12 Lawrence S. B. Goldstein, 16 Fangcheng Gong, 3 Ping Guan, 3 Nomi L. Harris, 12 Bruce A. Hay, 17 Roger A. Hoskins, 12 Jiayin Li, 3 Zhenya Li, 3 Richard O. Hynes, 18 S. J. M. Jones, 19 Peter M. Kuehl, 20 Bruno Lemaitre, 21 J. Troy Littleton, 22 Deborah K. Morrison, 23 Chris Mungall, 12 Patrick H. O'Farrell, 24 Oxana K. Pickeral, 10 Chris Shue, 3 Leslie B. Vosshall, 25 Jiong Zhang, 10 Qi Zhao, 3 Xiangqun H. Zheng, 3 Fei Zhong, 3 Wenyan Zhong, 3 Richard Gibbs, 26 J. Craig Venter, 3 Mark D. Adams, 3 Suzanna Lewis 2

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae--and the proteins they are predicted to encode--was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

1 Howard Hughes Medical Institute,
2 Department of Molecular and Cell Biology, Berkeley Drosophila Genome Project, University of California, Berkeley, CA 94720, USA.
3 Celera Genomics, Rockville, MD, 20850 USA.
4 GenetixXpress, 78 Pacific Road, Palm Beach, Sydney, Australia 2108.
5 Massachusetts General Hospital Cancer Center, Building 149, 13th Street, Charlestown, MA 02129 USA.
6 Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
7 EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
8 Department of Genetics, Stanford University, Palo Alto, CA 94305, USA.
9 Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
10 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
11 Neurogenetics Unit, Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
12 Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
13 Neomorphic, 2612 Eighth Street, Berkeley, CA 94710, USA.
14 School of Biology, University of Leeds, Leeds LS2 9JT, UK.
15 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
16 Departments of Cellular and Molecular Medicine and Pharmacology, Howard Hughes Medical Institute, University of California-San Diego, La Jolla, CA 92093, USA.
17 Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
18 Howard Hughes Medical Institute, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
19 Genome Sequence Centre, BC Cancer Research Centre, 600 West 10th Avenue, Vancouver, BC, V52 4E6, Canada.
20 Molecular and Cell Biology Program, University of Maryland at Baltimore, Baltimore, MD 21201, USA.
21 Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette, France.
22 Center for Learning and Memory, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
23 Regulation of Cell Growth Laboratory, Division of Basic Sciences, National Cancer Institute-Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, MD 21702, USA.
24 Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
25 Center for Neurobiology and Behavior, Columbia University, New York, NY 10032, USA.
26 Baylor College of Medicine Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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Genomic Background Drives the Divergence of Duplicated Amylase Genes at Synonymous Sites in Drosophila.
Z. Zhang and H. Kishino (2004)
Mol. Biol. Evol. 21, 222-227
   Abstract »    Full Text »    PDF »
Junctional adhesion molecules (JAMs): more molecules with dual functions?.
K. Ebnet, A. Suzuki, S. Ohno, and D. Vestweber (2004)
J. Cell Sci. 117, 19-29
   Abstract »    Full Text »    PDF »
Visual learning in individually assayed Drosophila larvae.
B. Gerber, S. Scherer, K. Neuser, B. Michels, T. Hendel, R. F. Stocker, and M. Heisenberg (2004)
J. Exp. Biol. 207, 179-188
   Abstract »    Full Text »    PDF »
The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity.
C. Vogel, S. A. Teichmann, and C. Chothia (2003)
Development 130, 6317-6328
   Abstract »    Full Text »    PDF »
Comparative Genomics and Structure Prediction of Dental Matrix Proteins.
R.K. Krishnaraju, T.C. Hart, and T.K. Schleyer (2003)
Advances in Dental Research 17, 100-103
   Abstract »    Full Text »    PDF »
The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans Genome.
V. Katju and M. Lynch (2003)
Genetics 165, 1793-1803
   Abstract »    Full Text »    PDF »
Correlations Between Gene Expression and Gene Conservation in Fission Yeast.
J. Mata and J. Bahler (2003)
Genome Res. 13, 2686-2690
   Abstract »    Full Text »    PDF »
Fly models of Huntington's disease.
J. L. Marsh, J. Pallos, and L. M. Thompson (2003)
Hum. Mol. Genet. 12, R187-193
   Abstract »    Full Text »    PDF »
An Evolutionary Analysis of Orphan Genes in Drosophila.
T. Domazet-Loso and D. Tautz (2003)
Genome Res. 13, 2213-2219
   Abstract »    Full Text »    PDF »
Genetic Analysis of the ADGF Multigene Family by Homologous Recombination and Gene Conversion in Drosophila.
T. Dolezal, M. Gazi, M. Zurovec, and P. J. Bryant (2003)
Genetics 165, 653-666
   Abstract »    Full Text »    PDF »
Functional Characterization and Expression Analysis of Members of the UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferase Family from Drosophila melanogaster.
K. G. Ten Hagen, D. T. Tran, T. A. Gerken, D. S. Stein, and Z. Zhang (2003)
J. Biol. Chem. 278, 35039-35048
   Abstract »    Full Text »    PDF »
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes.
L. Li, C. J. Stoeckert Jr., and D. S. Roos (2003)
Genome Res. 13, 2178-2189
   Abstract »    Full Text »    PDF »
Evolution of Insect Eye Development: First Insights from Fruit Fly, Grasshopper and Flour Beetle.
M. Friedrich (2003)
Integr. Comp. Biol. 43, 508-521
   Abstract »    Full Text »    PDF »


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