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The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
Open accessAbstract
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 difference is consistent with the lower gene number and reduced genome size in the urochordates (4).”
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Backgroundp53mRNA and p53 Protein Structures Have Evolved Independently to Interact with MDM2
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“…Sequencing and Analysis Consortium 2007; Warren et al. 2008 in platypus; Wade et al. 2009 in domestic horse; Aparicio et al. 2002 in pufferfish; International Chicken Genome Sequencing Consortium 2004; Kasahara et al. 2007 in medaka; Dehal et al. 2002 in Ciona; Putnam et al. 2008 in amphioxus).”
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“The genome sequence of the sea squirt Ciona intestinalis [1] shows the presence of closelyrelated genes, indicating that intelectins arose early in chordate evolution.”
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“*These authors contributed equally to this work ‡Authors for correspondence (yasuo@obs-vlfr.fr; yutaka@ascidian.zool.kyoto-u.ac.jp) Y.S., 0000-0001-5193-0708 D E V E LO P M E N T Gata.a directly activates Zic-r.b expression Zic-r.b is a multi-copy gene (Dehal et al., 2002; Yamada et al., 2003).”
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The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats
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“In the lower chordates, we verified that the genome of the tunicate sea squirt (27) (Ciona intestinalis) has a single GLS-like gene containing 12 exons.”
BackgroundThe Sea Squirt Ciona intestinalis: Figure 1.Preprint
Christiaen, L., Wagner, E., Shi, W., & Levine, M. (2009) · Cold Spring Harbor Protocols · doi:10.1101/pdb.emo138 · Cited by 29
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“In particular, genome-wide genetic research in various phylogenetically related animals conclusively facilitates evolutionary understanding (Dehal et al. 2002; Putnam et al. 2008; Simakov et al. 2015).”
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus
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“intestinalis genomic sequences [30], a number of positions with nucleotide differences were found in both the CDS and UTR of the sequenced transcript.”
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“html, (Dehal et al., 2002)).”
ResultThe animal in the genome: comparative genomics and evolution
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“For predicting proteins that emerged with vertebrates, we used the proteomes of Danio rerio (Howe et al. 2013), Xenopus tropicalis (Hellsten et al. 2010), and Gallus gallus (Groenen et al. 2000), and for tracing primate innovations, we used the Macaca mulatta proteome (Gibbs et al. 2007).”
MethodInfluentialFibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis
Segade, F., Cota, C. D., Famiglietti, A. L., Cha, A., & Davidson, B. (2016) · EvoDevo · doi:10.1186/s13227-016-0056-4 · Cited by 27
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BackgroundSelf-citationStructure, regulation, and function of micro1 in the sea urchin Hemicentrotus pulcherrimus
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“…purpuratus, Sodergren et al. 2006; Nematostella vectensis, Putnam et al. 2007; Branchiostoma floridae, Putnam et al. 2008; Ciona intestinalis, Dehal 2002; Ciona savignyi, Small et al. 2007; Homo sapiens, International Human Genome Sequencing Consortium et al. 2001; Mus musculus, Mouse…”
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Self-citation
Metadata
- 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
- Dehal, Paramvir
- Satou, Yutaka
- Degnan, Bernard
- Davidson, Brad
- Goodstein, David M.
- Harafuji, Naoe
- Hotta, Kohji
- Kawashima, Takeshi
- Lemaire, Patrick
- Martinez, Diego
- Meinertzhagen, Ian A.
- Saiga, Hidetoshi
- Terry, Astrid
- Wang, Hong-Gang
- Boore, Jeffrey
- Hino, Kyosuke
- Imai, Kaoru S.
- Inaba, Kazuo
- Kobayashi, Kenji
- Lee, Byung-In
- Manohar, Chitra
- Matassi, Giorgio
- Rigoutsos, Isidore
- Sasakura, Yasunori
- Shoguchi, Eiichi
- Stainier, Didier
- Suzuki, Miho M.
- Tassy, Olivier
- Tokuoka, Miki
- Doggett, Norman
- Kohara, Yuji
- Levine, Michael
- Rokhsar, Daniel S.
- Venue
- Science
- Published
- 2002-12-13
- Volume
- 298
- Issue
- 5601
- Pages
- 2157-2167
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- 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
- green
- hal.science
- 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
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › 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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