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Comparative Genomics of the Eukaryotes
Open accessAbstract
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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BackgroundMitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane
Haskins, N., Bhuvanendran, S., Anselmi, C., Gams, A., Kanholm, T., Kocher, K. M., LoTempio, J. E., Krohmaly, K. I., Sohai, D. K., Stearrett, N., et al. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2020.542950 · Cited by 31
Sharma, A., & Chauhan, R. S. (2012) · Comparative and Functional Genomics · doi:10.1155/2012/914843 · Cited by 31
Medina, P. M. B., Swick, L. L., Andersen, R., Blalock, Z., & Brenman, J. E. (2006) · Genetics · doi:10.1534/genetics.105.051276 · Cited by 31
“On the basis of a Poisson distribution with 76% of the lines that we generated carrying at least one lethalmutation, we estimate that we screened .5000 lethal mutations compared to a total gene estimate of 13,000 in Drosophila (Rubin et al. 2000).”
BackgroundMolecular Genetic Analysis of Ethanol Intoxication in Drosophila melanogaster
Heberlein, U. (2004) · Integrative and Comparative Biology · doi:10.1093/icb/44.4.269 · Cited by 31
Xiu-mei, M. (2005) · World Journal of Gastroenterology · doi:10.3748/wjg.v11.i42.6716 · Cited by 31
Siomi, H., Ishizuka, A., & Siomi, M. C. (2004) · Mental Retardation and Developmental Disabilities Research Reviews · doi:10.1002/mrdd.20011 · Cited by 31
“Many genes are conserved between flies and humans, including genes that regulate complex behaviors such as learning and memory and circadian rhythms, as well as entire pathways of development and oncogenesis [Patel, 1994; Miklos and Rubin, 1996; Rubin et al., 2000].”
BackgroundFunctional studies of the BTB domain in the Drosophila GAGA and Mod(mdg4) proteins
Read, D. B. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.20.3864 · Cited by 31
The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants
Thornton, K. (2007) · Genetics · doi:10.1534/genetics.107.074948 · Cited by 32
“Comparative genome sequencing has revealed that distantly related organisms, such as flies, worms, yeast, and humans, have roughly similar gene numbers, but that the sizes of individual gene families vary across organisms (Rubin et al. 2000).”
BackgroundSorting and transport in C. elegans: a model system with a sequenced genome
Koushika, S. P., & Nonet, M. L. (2000) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(00)00125-3 · Cited by 31
Yeast Two-Hybrid Systems and Protein Interaction Mapping Projects for Yeast and Worm
Walhout, A. J. M., Boulton, S. J., & Vidal, M. (2000) · Yeast · doi:10.1155/2000/156745 · Cited by 31
Toxicogenomics: "The Call of the Wild Chip"
Iannaccone, P. M. (2001) · Environmental Health Perspectives · doi:10.1289/ehp.109-a8 · Cited by 31
Drosophila as a Model for Human Disease: Insights into Rare and Ultra-Rare Diseases
Casas‐Tintó, S. (2024) · Insects · doi:10.3390/insects15110870 · Cited by 39
Carlson, K. A., Gardner, K., Pashaj, A., Carlson, D. J., Yu, F., Eudy, J. D., Zhang, C., & Harshman, L. G. (2015) · Genetics Research International · doi:10.1155/2015/835624 · Cited by 28
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.
What counts as a claim ›How we measure confidence ›How we check this ›
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