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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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“The fruit fly has obvious advantages as a diabetes model: (1) it is small and can be easily raised in large quantities in the laboratory (8); (2) it has a short life-cycle (10–12 days) and thus it is the data results of certain studies based on it that can be obtained quickly; (3) it has complex neuropils and neural c…”
BackgroundSelf-citationKembro, J. M., Flesia, A. G., Nieto, P. S., Caliva, J. M., Lloyd, D., Cortassa, S. C., & Aon, M. A. (2023) · Scientific Reports · doi:10.1038/s41598-023-32286-0 · Cited by 16
Drosophila as a Robust Model System for Assessing Autophagy: A Review
Demir, E., & Kacew, S. (2023) · Toxics · doi:10.3390/toxics11080682 · Cited by 18
Berglund, E. C., Kuklinski, N. J., Karagündüz, E., Ucar, K., Hanrieder, J., & Ewing, A. G. (2013) · Analytical Chemistry · doi:10.1021/ac303377x · Cited by 17
Galea, C. A., Mobli, M., McNeil, K. A., Mulhern, T. D., Wallace, J. C., King, G. F., Forbes, B. E., & Norton, R. S. (2011) · Biochimie · doi:10.1016/j.biochi.2011.09.012 · Cited by 17
Molecular Alterations in Sporadic Primary Hyperparathyroidism
Alvelos, M. I., Mendes, M., & Soares, P. (2011) · Genetics Research International · doi:10.4061/2011/275802 · Cited by 17
Castillo-Morales, A., Monzón‐Sandoval, J., Urrutia, A. O., & Gutiérrez, H. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.2428 · Cited by 17
Gene duplication in the genome of parasitic Giardia lamblia
Sun, J., Jiang, H., Flores, R., & Wen, J. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-49 · Cited by 18
Picchio, L., Legagneux, V., Deschamps, S., Renaud, Y., Chauveau, S., Paillard, L., & Jagla, K. (2018) · Disease Models & Mechanisms · doi:10.1242/dmm.031849 · Cited by 17
Strategies for Engineering and Rewiring Kinase Regulation
McCormick, J. W., Pincus, D., Resnekov, O., & Reynolds, K. A. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.11.005 · Cited by 17
The Globin Gene Family in Arthropods: Evolution and Functional Diversity
Prothmann, A., Hoffmann, F. G., Opazo, J. C., Herbener, P., Storz, J. F., Burmester, T., & Hankeln, T. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00858 · Cited by 17
“Thus, in contrast to early interpretations of comparative genome analyses (Rubin et al., 2000), our results indicate that globins are part of the standard gene repertoire of the arthropod genome.”
ResultExploring the alternative: Fish, flies and worms as preclinical models for ALS
Braems, E., Tziortzouda, P., & Bosch, L. V. D. (2021) · Neuroscience Letters · doi:10.1016/j.neulet.2021.136041 · Cited by 20
Mingione, V. R., Foda, Z. H., Paung, Y., Philipose, H., Rangwala, A. M., Shan, Y., & Seeliger, M. A. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167628 · Cited by 13
Collins, A. G. (2000) · doi:10.1666/0094-8373(2000)026
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
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