Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
Open accessAbstract
Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
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Introns shared between Nematostella and vertebrates and/or other bilaterians are most parsimoniously interpreted as conserved ancient eumetazoan introns.
“Introns that are shared between Nematostella and vertebrates and/or other bilaterians are most parsimoniously interpreted as conserved ancient eumetazoan introns (44).”
From Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization (2007) · cites this paper as [44]
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- Authors
- Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., Dossat, C., Segurens, B., Dasilva, C., Salanoubat, M., Levy, M., Boudet, N., Castellano, S., Anthouard, V., Jubin, C., Castelli, V., Katinka, M., Vacherie, B., Biémont, C., Skalli, Z., Cattolico, L., Poulain, J., de Berardinis, V., Cruaud, C., Duprat, S., Brottier, P., Coutanceau, J.-P., Gouzy, J., Parra, G., Lardier, G., Chapple, C., McKernan, K. J., McEwan, P., Bosak, S., Kellis, M., Volff, J.-N., Guigó, R., Zody, M. C., Mesirov, J., Lindblad-Toh, K., Birren, B., Nusbaum, C., Kahn, D., Robinson-Rechavi, M., Laudet, V., Schachter, V., Quétier, F., Saurin, W., Scarpelli, C., Wincker, P., Lander, E. S., Weissenbach, J., & Roest Crollius, H.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- École Normale Supérieure de Lyon (FR)
- Broad Institute (US)
- Universitat Pompeu Fabra (ES)
- Lyon 1 Université (FR)
- University of Würzburg (DE)
- Corresponding author
- Weissenbach, Jean
- ORCID
- Jaillon, Olivier
- Aury, Jean-Marc
- Brunet, Frédéric
- Petit, Jean-Louis
- Jaffe, David
- Lutfalla, Georges
- Salanoubat, Marcel
- Castellano, Sergi
- Vacherie, Benoît
- Poulain, Julie
- Cruaud, Corinne
- Duprat, Simone
- Gouzy, Jérôme
- McKernan, Kevin J.
- Kellis, Manolis
- Volff, Jean-Nicolas
- Guigó, Roderic
- Zody, Michael C.
- Mesirov, Jill
- Birren, Bruce
- Nusbaum, Chad
- Kahn, Daniel
- Laudet, Vincent
- Scarpelli, Claude
- Wincker, Patrick
- Lander, Eric S.
- Weissenbach, Jean
- Venue
- Nature
- Published
- 2004-10
- Volume
- 431
- Issue
- 7011
- Pages
- 946-957
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2064912476
- Cited by
- 1,966
- References
- 60
- Citations by year
- 2026: 33 · 2025: 38 · 2024: 47 · 2023: 46 · 2022: 69 · 2021: 61 · 2020: 74 · 2019: 83 · 2018: 73 · 2017: 85 · 2016: 76 · 2015: 90 · 2014: 93 · 2013: 93 · 2012: 110
- FWCI
- 154.78
- Type
- journal article
- Language
- en
- Open access
- green
- hal.inrae.fr
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Broad Institute
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Tetraodon nigroviridis, whole-genome duplication, karyotype evolution, chromosomal rearrangements, genome annotation, gene family divergence, genome anchoring
- MeSH terms
- Animals, Base Composition, Chromosomes, Chromosomes, Human, Fishes, Genes, Humans, Karyotyping, Mammals, Models, Genetic, Molecular Sequence Data, Urochordata, Vertebrates, Genome, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Physical Chromosome Mapping, Gene Duplication, Proteome, Synteny
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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