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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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In Vivo Structure/Function Analysis of the Drosophila fat facets Deubiquitinating Enzyme Gene
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“Over 50% of fly genes exhibit apparent homology to human genes, with conservation of molecular mechanisms and fundamental aspects of cell biology including regulation of gene expression, neuronal connectivity, cell signalling and cell death (Adams et al. 2000; Rubin et al. 2000).”
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“Protein kinase domains are found in ~2% of eukaryotic genes [1], which also reflects their importance.”
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Many Light Touches Convey the Message
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Nematicidal effects of hemp ( Cannabis sativa ) may not be mediated by cannabinoid receptors
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Taking a functional genomics approach in molecular medicine
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Fungal Zuotin Proteins Evolved from MIDA1-like Factors by Lineage-Specific Loss of MYB Domains
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“Similarity of domain structures has also been used as information for assigning orthology (Huynen and Bork 1998), a method especially helpful for large-scale genomic comparisons (e.g., Rubin et al. 2000).”
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Sequence Analysis of the Human Genome
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“In addition, 12 GABAA/glycine-like receptor subunit genes have been recently identified in the D. melanogaster genome (Rubin et al. 2000) confirming the existence of a multiplicity of GABA receptor subunits in insects.”
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“A comparison of 300 human disease-associated genes shows that almost 80% have an ortholog in the insect Drosophila melanogaster, 70% have an ortholog in the nematode Caenorhabditis elegans [ 14 ] and Arabidopsis still possesses orthologs for 60% of thesehuman disease-associated genes(http://mipsgsfde/proj/thal/ db/tab…”
BackgroundFungi and humans: closer than you think
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Self-citationStudying alcohol use disorder using Drosophila melanogaster in the era of ‘Big Data’
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Self-citationApplications of yeast in drug discovery
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A maturing understanding of the composition of the insect gene repertoire
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“Comparisons with the only two other sequenced eukaryotes at the time identified worm orthologues for about 30% of fly genes and a conserved core of about 20% with orthologues in both worm and yeast [3].”
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Effects of lithium chloride on the gene expression profiles in Drosophila heads
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“In part, this is due to the fact that Drosophila and higher vertebrates share genetic pathways for cellular signaling (Miklos and Rubin, 1996; Rubin et al., 2000).”
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Interactive nervous system development: control of cell survival in Drosophila
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The Effects of Royal Jelly on Fitness Traits and Gene Expression in Drosophila melanogaster
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“Subsequently, the Berkeley Drosophila Genome Project revealed the presence of four Hsp60-like DNA sequences at different cytogenetic positions (Adams et al., 2000, Rubin et al., 2000).”
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“More putative subunits are predicted from sequence analysis of the Drosophila genome (Rubin et al. 2000).”
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“Drosophila is an excellent system to study tumorigenesis, because many human oncogenic genes and tumor suppressor genes are conserved (Banfi et al. 1996; Rubin et al. 2000; Ito et al. 2014).”
BackgroundVariation across Species and Levels: Implications for Model Species Research
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Flying Together: Drosophila as a Tool to Understand the Genetics of Human Alcoholism
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“Most mammalian genes have orthologs in flies [27], including all major human gene families [28].”
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Inhibition of Cellular Functions of HIV-1 Nef by Artificial SH3 Domains
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“Thereafter SH3 domains have been noticed in a large number of proteins, and a total of 63 SH3 domains were found in the fruit fly genome (Rubin et al., 2000), while more than 200 human proteins with SH3 domains can currently be found from the SwissProt database (using SMART; Schultz et al., 1998).”
BackgroundPlants as models for the study of human pathogenesis
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Warren, C. E., Krizus, A., & Dennis, J. W. (2001) · Glycobiology · doi:10.1093/glycob/11.11.979 · Cited by 25
“A characteristic of metazoan radiation is the duplication of genomic blocks resulting in the appearance of multiple diverged homologues of ancestral precursors (Rubin et al., 2000).”
BackgroundMethodInfluentialDecoding the human genome sequence
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Genetic regulation of programmed cell death in Drosophila
Lee, C., & Baehrecke, E. H. (2000) · Cell Research · doi:10.1038/sj.cr.7290048 · Cited by 25
Dolezal, T., Gaži, M., Žurovec, M., & Bryant, P. J. (2003) · Genetics · doi:10.1093/genetics/165.2.653 · Cited by 25
“…5000 genes in the Drosophila genome appear mechanism, depleting the levels of extracellular adeno-sine that otherwise have a negative effect on growth ofto have arisen by gene duplication and are now members of multigene families (Rubin et al. 2000), rais- several cell types (Zurovec et al. 2002).”
BackgroundAusten, B., Frears, E. R., & Davies, H. (2000) · Journal of Peptide Science · doi:10.1002/1099-1387(200009)6:9 · Cited by 70
Cloning, Expression, and Mapping of hWW45, a Novel Human WW Domain-Containing Gene
Valverde, P. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.3582 · Cited by 25
Functional Genomics of Odor-guided Behavior in Drosophila melanogaster
Anholt, R. R. H. (2001) · Chemical Senses · doi:10.1093/chemse/26.2.215 · Cited by 25
Detection of gene duplications and block duplications in eukaryotic genomes
Li, W., Gu, Z., Cavalcanti, A. R. O., & Nekrutenko, A. (2003) · Journal of Structural and Functional Genomics · doi:10.1023/a:1022644628861 · Cited by 25
Simonet, G., Claeys, I., November, T., Wataleb, S., Janssen, T. A. H., Maes, R., LOOF, A. D., & Broeck, J. V. (2002) · Insect Molecular Biology · doi:10.1046/j.1365-2583.2002.00345.x · Cited by 25
“The recent elucidation of the fruit fly genome has revealed the enormous diversity of insect proteases compared to worms and yeast (Rubin et al., 2000).”
BackgroundBeenomes to Bombyx: future directions in applied insect genomics.
Evans, J. D., & Gundersen‐Rindal, D. E. (2003) · Genome biology · doi:10.1186/gb-2003-4-3-107 · Cited by 24
Targeted Mutagenesis of Duplicated Genes in Caenorhabditis elegans Using CRISPR-Cas9
Xu, S., Wang, Z., Kim, K. W., Jin, Y., & Chisholm, A. D. (2016) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2015.11.004 · Cited by 24
“It has been estimated that about 1/3 of genes in the C. elegans genome are either duplicated or members of closely related gene families (Cavalcanti et al., 2003; Rubin et al., 2000).”
BackgroundModeling congenital disease and inborn errors of development inDrosophila melanogaster
Moulton, M. J., & Letsou, A. (2016) · Disease Models & Mechanisms · doi:10.1242/dmm.023564 · Cited by 28
Roethele, J. B., Romero‐Severson, J., & Feder, J. L. (2001) · Annals of the Entomological Society of America · doi:10.1603/0013-8746(2001)094[0936:efbsco]2.0.co;2 · Cited by 24
Royet, J. (2004) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-003-3243-0 · Cited by 24
Lasko, P. F. (2002) · Clinical Genetics · doi:10.1034/j.1399-0004.2002.620502.x · Cited by 23
Statistics of the Numbers of Transcripts and Protein Sequences Encoded in the Genome
Kuznetsov, V. A. (2005) · Kluwer Academic Publishers eBooks · doi:10.1007/0-306-47825-0_9 · Cited by 24
The FAR protein family of parasitic nematodes
Parks, S. C., Nguyen, S. T., Boulanger, M. J., & Dillman, A. R. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010424 · Cited by 23
“One unique protein family in nematode ESPs is the family of fatty acid–and retinol-binding proteins (FARs) [7].”
BackgroundTemperature and Urea Have Opposing Impacts on Polyproline II Conformational Bias
Elam, W. A., Schrank, T. P., Campagnolo, A. J., & Hilser, V. J. (2013) · Biochemistry · doi:10.1021/bi301435p · Cited by 23
Whole-genome expression profile analysis of Drosophila melanogaster immune responses
Teixeira, L. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els043 · Cited by 23
Behavior in a Drosophila Model of Fragile X
McBride, S. M. J., Bell, A. J., & Jongens, T. A. (2011) · Results and problems in cell differentiation · doi:10.1007/978-3-642-21649-7_6 · Cited by 24
Cellular identity at the single-cell level
Coskun, A. F., Eser, U., & Islam, S. (2016) · Molecular BioSystems · doi:10.1039/c6mb00388e · Cited by 24
Novel genetic approaches to behavior in Drosophila
Martín, F., & Alcorta, E. (2017) · Journal of Neurogenetics · doi:10.1080/01677063.2017.1395875 · Cited by 23
Innate Immunity in Fruit Flies: A Textbook Example of Genomic Recycling
Govind, S., & Nehm, R. H. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020276 · Cited by 23
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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