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Cited by 1,641Developmental Biology and Gene RegulationGenomics and Phylogenetic StudiesMarine Invertebrate Physiology and Ecology

The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins

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Dehal, Paramvir, Satou, Yutaka, Campbell, Robert K., Chapman, Jarrod, Degnan, Bernard, De Tomaso, Anthony, Davidson, Brad, Di Gregorio, Anna +79 more·2002·Science
DOI 10.1126/science.1080049
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Abstract

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis . The Ciona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona , suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

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  • The lower ortholog counts for ascidian are consistent with the lower gene number and reduced genome size in urochordates.

    “The difference is consistent with the lower gene number and reduced genome size in the urochordates (4).”

    From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [4]

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Authors
Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D. M., Harafuji, N., Hastings, K. E. M., Ho, I., Hotta, K., Huang, W., Kawashima, T., Lemaire, P., Martinez, D., Meinertzhagen, I. A., Necula, S., Nonaka, M., Putnam, N., Rash, S., Saiga, H., Satake, M., Terry, A., Yamada, L., Wang, H.-G., Awazu, S., Azumi, K., Boore, J., Branno, M., Chin-bow, S., DeSantis, R., Doyle, S., Francino, P., Keys, D. N., Haga, S., Hayashi, H., Hino, K., Imai, K. S., Inaba, K., Kano, S., Kobayashi, K., Kobayashi, M., Lee, B.-I., Makabe, K. W., Manohar, C., Matassi, G., Medina, M., Mochizuki, Y., Mount, S., Morishita, T., Miura, S., Nakayama, A., Nishizaka, S., Nomoto, H., Ohta, F., Oishi, K., Rigoutsos, I., Sano, M., Sasaki, A., Sasakura, Y., Shoguchi, E., Shin-i, T., Spagnuolo, A., Stainier, D., Suzuki, M. M., Tassy, O., Takatori, N., Tokuoka, M., Yagi, K., Yoshizaki, F., Wada, S., Zhang, C., Hyatt, P. D., Larimer, F., Detter, C., Doggett, N., Glavina, T., Hawkins, T., Richardson, P., Lucas, S., Kohara, Y., Levine, M., Satoh, N., & Rokhsar, D. S.
Affiliations
  • Joint Genome Institute (US)
  • Kyoto University (JP)
  • Marine Biological Laboratory (US)
  • The University of Queensland (AU)
  • Department of Pathology, Stanford University School of Medicine, Stanford, CA 93950, USA.
  • University of California, Berkeley (US)
  • Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA.
  • McGill University (CA)
  • National Institute of Genetics (JP)
  • Institut de Biologie du Développement Marseille (FR)
  • Dalhousie University (CA)
  • The University of Tokyo (JP)
  • U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
  • Tokyo Metropolitan University (JP)
  • Tohoku University (JP)
  • Moffitt Cancer Center (US)
  • Hokkaido University (JP)
  • Stazione Zoologica Anton Dohrn (IT)
  • IBM (United States) (US)
  • University of Maryland, College Park, MD 20742, USA.
  • National Institute of Genetics, Mishima 411-8540, Japan.
  • Stazione Zoologica “Anton Dohrn,” Villa Comunale, 80121 Napoli, Italy.
  • University of California, San Francisco (US)
  • Wellcome Centre for Cell Biology (GB)
  • Oak Ridge National Laboratory, Post Office Box 2008, Oak Ridge, TN 37831, USA.
  • Oak Ridge National Laboratory (US)
  • Los Alamos National Laboratory (US)
Corresponding author
  • Dehal, Paramvir
  • Satou, Yutaka
  • Kohara, Yuji
  • Levine, Michael
  • Satoh, Nori
  • Rokhsar, Daniel S.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2002-12-13
Volume
298
Issue
5601
Pages
2157-2167
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1080049
OpenAlex
W2170258388
Cited by
1,641
References
81
Citations by year
2026: 20 · 2025: 15 · 2024: 41 · 2023: 26 · 2022: 27 · 2021: 36 · 2020: 41 · 2019: 29 · 2018: 51 · 2017: 49 · 2016: 43 · 2015: 46 · 2014: 62 · 2013: 62 · 2012: 74
FWCI
49.61
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • HAL AMU (submittedVersion, cc-by-nc)
  • Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
Funders
  • National Institutes of Health (5p01hd037105-20)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD37105)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
Keywords
Ciona intestinalis, chordate evolution, vertebrate origin, gene family evolution, protein-coding genes, gene loss, developmental genes, Cambrian explosion
MeSH terms
Alleles, Animals, Base Sequence, Cellulose, Central Nervous System, Ciona intestinalis, Endocrine System, Genes, Genes, Homeobox, Multigene Family, Heart, Immunity, Molecular Sequence Data, Muscle Proteins, Phylogeny, Polymorphism, Genetic, Proteins, Sequence Homology, Nucleic Acid, Species Specificity, Thyroid Gland, Urochordata, Vertebrates, Genome, Apoptosis, Sequence Analysis, DNA, Gene Dosage, Computational Biology, Gene Duplication, Organizers, Embryonic

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