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Comparative Genomics of the Eukaryotes
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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.
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“To our knowledge, this is the first genome-wide survey and comparison of conserved elements in different groups of eukaryotic species (excluding comparisons primarily of proteomes; e.g., Rubin et al. 2000).”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Rubin et al. 2000
In the citing paper
“Comparisons (4-6) between fruit fly, nematode, and vertebrate genomes reveal greater genomic complexity in the vertebrates (and other deuterostomes (7,8)) as measured by gene content and structure, but at the same time show that many genes and networks are shared across bilaterians.”
From Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization (2007) · cites this paper as [4]
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Desaturases fused to their electron donor
Sperling, P., & Heinz, E. (2001) · European Journal of Lipid Science and Technology · doi:10.1002/1438-9312(200103)103:3 · Cited by 72
Blasie, C. A., & Berg, J. M. (2002) · Biochemistry · doi:10.1021/bi026621h · Cited by 73
Schizosaccharomyces pombe Essential Genes: A Pilot StudyPreprint
Decottignies, A., Sánchez‐Pérez, I., & Nurse, P. (2003) · Genome Research · doi:10.1101/gr.636103 · Cited by 73
“It has been suggested that these proteins may be required for more specialized functions (Chervitz et al. 1998; Rubin et al. 2000).”
BackgroundPhylogenomics reveal a robust fungal tree of life
Kuramae, E. E., Robert, V., Snel, ., Weiß, M., & Boekhout, T. (2006) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2006.00119.x · Cited by 71
Linking DNA-binding proteins to their recognition sequences by using protein microarrays
Ho, S.-W., Jona, G., Chen, C. T. L., Johnston, M., & Snyder, M. P. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509185103 · Cited by 70
Mechanism of Mss116 ATPase Reveals Functional Diversity of DEAD-Box Proteins
Cao, W., Coman, M. M., Ding, S. C., Henn, A., Middleton, E. R., Bradley, M. J., Rhoades, E. R., Hackney, D. D., Pyle, A. M., & Cruz, E. M. D. L. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.004 · Cited by 71
Drosophila melanogaster and the development of biology in the 20th century.
Arias, A. M. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-583-1_1 · Cited by 72
Crystal structure and mutational analysis of a perlecan-binding fragment of nidogen-1.
Hopf, M., Göhring, W., Ries, A., Timpl, R., & Hohenester, E. (2001) · Nature Structural Biology · doi:10.1038/89683 · Cited by 71
Common Mechanism of Ligand Recognition by Group II/III WW Domains
Kato, Y. S., Nagata, K., Takahashi, M., Lian, L., Herrero, J. J., Sudol, M., & Tanokura, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m404719200 · Cited by 71
PLANT GENOMICS: The Third Wave
Borevitz, J., & Ecker, J. R. (2004) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.5.061903.180017 · Cited by 71
“gov/COG/) (138) and several initial genome-wide comparative studies (25, 117, 140) relied on all-against-all BLAST searches.”
MethodJiang, J., & White‐Cooper, H. (2003) · Development · doi:10.1242/dev.00246 · Cited by 70
“…so is expressed throughout development (Lehner and O’Farrell, 1990), twineis required for meiosis in the female germline so is also expressed in ovaries (Alphey et al., 1992), and boule transcripts have been found in cDNA libraries derived from heads (H. W.-C., unpublished) (Rubin et al., 2000).”
BackgroundGreen, R. B., Hatini, V., Johansen, K. A., Liu, X., & Lengyel, J. A. (2002) · Development · doi:10.1242/dev.129.15.3645 · Cited by 70
Modafinil Maintains Waking in the Fruit Fly Drosophila Melanogaster
Hendricks, J. C., Kirk, D., Panckeri, K. A., Miller, M. S., & Pack, A. I. (2003) · SLEEP · doi:10.1093/sleep/26.2.139 · Cited by 70
The interrelationship of proteasome impairment and oligomeric intermediates in neurodegeneration
Deger, J. M., Gerson, J. E., & Kayed, R. (2015) · Aging Cell · doi:10.1111/acel.12359 · Cited by 69
“Although the data from this model have provided no evidence that a synuclein homolog exists (Rubin et al., 2000), these flies express human asynuclein more readily than transgenic mice, suggesting that vertebrates or possibly mammals have developed mechanisms that prevent asynuclein assembly.”
Background
Metadata
- Authors
- Rubin, G. M., Yandell, M. D., Wortman, J. R., Gabor, G. L., Miklos, Nelson, C. R., Hariharan, I. K., Fortini, M. E., Li, P. W., Apweiler, R., Fleischmann, W., Cherry, J. M., Henikoff, S., Skupski, M. P., Misra, S., Ashburner, M., Birney, E., Boguski, M. S., Brody, T., Brokstein, P., Celniker, S. E., Chervitz, S. A., Coates, D., Cravchik, A., Gabrielian, A., Galle, R. F., Gelbart, W. M., George, R. A., Goldstein, L. S. B., Gong, F., Guan, P., Harris, N. L., Hay, B. A., Hoskins, R. A., Li, J., Li, Z., Hynes, R. O., Jones, S. J. M., Kuehl, P. M., Lemaitre, B., Littleton, J. T., Morrison, D. K., Mungall, C., O'Farrell, P. H., Pickeral, O. K., Shue, C., Vosshall, L. B., Zhang, J., Zhao, Q., Zheng, X. H., Zhong, F., Zhong, W., Gibbs, R., Venter, J. C., Adams, M. D., & Lewis, S.
- Affiliations
- Howard Hughes Medical Institute (US)
- Celera Genomics, Rockville, MD, 20850 USA.
- GenetixXpress, 78 Pacific Road, Palm Beach, Sydney, Australia 2108.
- University of California, Berkeley (US)
- Harvard University (US)
- University of Pennsylvania (US)
- European Bioinformatics Institute (GB)
- Stanford University (US)
- Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa (ZA)
- National Institutes of Health (US)
- Lawrence Berkeley National Laboratory (US)
- Neomorphic, 2612 Eighth Street, Berkeley, CA 94710, USA.
- University of Leeds (GB)
- California Institute of Technology (US)
- BC Cancer Agency (CA)
- University of Maryland, Baltimore (US)
- Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette, France.
- Massachusetts Institute of Technology (US)
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
- Columbia University (US)
- Baylor College of Medicine (US)
- ORCID
- Rubin, Gerald M.
- Yandell, Mark D.
- Wortman, Jennifer R.
- Nelson, Catherine R.
- Hariharan, Iswar K.
- Apweiler, Rolf
- Cherry, J. Michael
- Henikoff, Steven
- Ashburner, Michael
- Birney, Ewan
- Celniker, Susan E.
- Chervitz, Stephen A.
- Gabrielian, Andrei
- George, Reed A.
- Goldstein, Lawrence S. B.
- Guan, Ping
- Harris, Nomi L.
- Hay, Bruce A.
- Li, Jiayin
- Hynes, Richard O.
- Jones, S. J. M.
- Littleton, J. Troy
- Morrison, Deborah K.
- Mungall, Chris
- Vosshall, Leslie B.
- Zhang, Jiong
- Zhao, Qi
- Zhong, Fei
- Zhong, Wenyan
- Gibbs, Richard
- Venter, J. Craig
- Adams, Mark D.
- Lewis, Suzanna
- Venue
- Science
- Published
- 2000-03-24
- Volume
- 287
- Issue
- 5461
- Pages
- 2204-2215
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2754258
- OpenAlex
- W2106013076
- Cited by
- 1,698
- References
- 87
- Citations by year
- 2026: 19 · 2025: 26 · 2024: 18 · 2023: 24 · 2022: 30 · 2021: 29 · 2020: 37 · 2019: 33 · 2018: 36 · 2017: 34 · 2016: 34 · 2015: 38 · 2014: 34 · 2013: 45 · 2012: 55
- FWCI
- 75.40
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- National Human Genome Research Institute (P50HG000750, P4IHG00739, P50-HG00750)
- National Institute of General Medical Sciences (R01GM037193, R01GM060988)
- National Institute of Neurological Disorders and Stroke (R01NS040296)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- comparative genomics, eukaryotic genomes, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, gene family expansion, multidomain proteins, signaling pathways, orthologs, human disease genes, model organisms
- MeSH terms
- Animals, Cell Adhesion, Cell Cycle, Drosophila melanogaster, Biological Evolution, Fungal Proteins, Multigene Family, Genetics, Medical, Humans, Immunity, Neoplasms, Saccharomyces cerevisiae, Signal Transduction, Helminth Proteins, Genome, Caenorhabditis elegans, Apoptosis, Protein Structure, Tertiary, Insect Proteins, Genes, Duplicate, Proteome, Genetic Diseases, Inborn
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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