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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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BackgroundDrosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation
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BackgroundFactors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae
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BackgroundRapid Evolution of Coral Proteins Responsible for Interaction with the Environment
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“[107] Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK.”
BackgroundKallmann syndrome: towards molecular pathogenesis
Hardelin, J. (2001) · Molecular and Cellular Endocrinology · doi:10.1016/s0303-7207(01)00462-2 · Cited by 100
Babula-Skowrońska, D., Kaczmarek, M., Barakat, A., Delseny, M., Quirós, C. F., & Sadowski, J. (2003) · Molecular Genetics and Genomics · doi:10.1007/s00438-002-0782-2 · Cited by 98
“Such examples of opposite orientation of adjacent gene duplications have already been reported in A. thaliana (Ku et al. 2000) and in Drosophila melanogaster (Rubin et al. 2000).”
BackgroundGrech, A. P., Quinn, R., Srinivasan, D., Badoux, X. C. A., & Brink, R. A. (2000) · Molecular Immunology · doi:10.1016/s0161-5890(00)00098-5 · Cited by 98
Lewis, S., Ashburner, M., & Reese, M. G. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00095-6 · Cited by 98
Self-citationPhylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules
Ruprecht, C., Proost, S., Hernández-Coronado, M., Ortiz‐Ramírez, C., Lang, D., Rensing, S. A., Becker, J. D., Vandepoele, K., & Mutwil, M. (2017) · The Plant Journal · doi:10.1111/tpj.13502 · Cited by 93
Three multigene families in Plasmodium parasites: facts and questions
Mercereau‐Puijalon, O., Barale, J.-C., & Bischoff, E. (2002) · International Journal for Parasitology · doi:10.1016/s0020-7519(02)00111-x · Cited by 97
Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling
Mills, J. D., Kawahara, Y., & Janitz, M. (2013) · Current Genomics · doi:10.2174/1389202911314030003 · Cited by 97
Shyu, Y. J., Hiatt, S. M., Duren, H. M., Ellis, R. E., Kerppola, T. K., & Hu, C. (2008) · Nature Protocols · doi:10.1038/nprot.2008.16 · Cited by 96
Parkinsons Disease and other α-Synucleinopathies
Goedert, M. (2001) · Clinical Chemistry and Laboratory Medicine · doi:10.1515/cclm.2001.047 · Cited by 96
In vivo assessment of CdSe-ZnS quantum dots: coating dependent bioaccumulation and genotoxicity.
Galeone, A., Vecchio, G., Malvindi, M., Brunetti, V., Cingolani, R., & Pompa, P. (2012) · Nanoscale · doi:10.1039/c2nr31826a · Cited by 93
Enzymes of Sphingolipid metabolism in Drosophila melanogaster
Acharya, U. R., & Acharya, J. (2005) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-004-4254-1 · Cited by 95
Intestinal Epithelial Wnt Signaling Mediates Acetylcholine-Triggered Host Defense against Infection
Labed, S. A., Wani, K. A., Jagadeesan, S., Hakkim, A., Najibi, M., & Irazoqui, J. E. (2018) · Immunity · doi:10.1016/j.immuni.2018.04.017 · Cited by 98
“In C. elegans, the GPCR superfamily is greatly expanded (Rubin et al., 2000).”
Drosophila as a screening tool to study human neurodegenerative diseases
Lenz, S., Karsten, P., Schulz, J. B., & Voigt, A. (2013) · Journal of Neurochemistry · doi:10.1111/jnc.12446 · Cited by 101
“Owing to the small and by now fully sequenced genome of flies (Adams et al. 2000; Rubin et al. 2000), large-scale screening approaches are easy to perform.”
BackgroundAhn, J. C., Kim, D.-W., You, Y. N., Seok, M. S., Park, J. M., Hwang, H., Kim, B., Luan, S., Park, H.-S., & Cho, H. S. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-253 · Cited by 94
Zhao, Z., Sheps, J. A., Ling, V. W. T., Fang, L. L., & Baillie, D. L. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.052 · Cited by 94
Babu, M., Griffiths, J. S., Huang, T.-S., & Wang, A. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-325 · Cited by 93
Functional Diversity in Neuronal Voltage-Gated Calcium Channels by Alternative Splicing of Cavα1
Lipscombe, D., Pan, J. Q., & Gray, A. C. (2002) · Molecular Neurobiology · doi:10.1385/mn:26:1:021 · Cited by 93
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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