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Science 13 December 2002:
Vol. 298. no. 5601, pp. 2157 - 2167
DOI: 10.1126/science.1080049
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Research Articles

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

Paramvir Dehal,1* Yutaka Satou,2* Robert K. Campbell,34 Jarrod Chapman,1 Bernard Degnan,5 Anthony De Tomaso,6 Brad Davidson,7 Anna Di Gregorio,7 Maarten Gelpke,1 David M. Goodstein,1 Naoe Harafuji,7 Kenneth E. M. Hastings,8 Isaac Ho,1 Kohji Hotta,9 Wayne Huang,1 Takeshi Kawashima,10 Patrick Lemaire,11 Diego Martinez,1 Ian A. Meinertzhagen,12 Simona Necula,1 Masaru Nonaka,13 Nik Putnam,1 Sam Rash,1 Hidetoshi Saiga,14 Masanobu Satake,15 Astrid Terry,1 Lixy Yamada,2 Hong-Gang Wang,16 Satoko Awazu,2 Kaoru Azumi,17 Jeffrey Boore,1 Margherita Branno,18 Stephen Chin-bow,19 Rosaria DeSantis,18 Sharon Doyle,1 Pilar Francino,1 David N. Keys,17 Shinobu Haga,9 Hiroko Hayashi,9 Kyosuke Hino,2 Kaoru S. Imai,2 Kazuo Inaba,20 Shungo Kano,218 Kenji Kobayashi,2 Mari Kobayashi,2 Byung-In Lee,1 Kazuhiro W. Makabe,2 Chitra Manohar,1 Giorgio Matassi,18 Monica Medina,1 Yasuaki Mochizuki,2 Steve Mount,21 Tomomi Morishita,9 Sachiko Miura,9 Akie Nakayama,2 Satoko Nishizaka,9 Hisayo Nomoto,9 Fumiko Ohta,9 Kazuko Oishi,9 Isidore Rigoutsos,19 Masako Sano,9 Akane Sasaki,2 Yasunori Sasakura,2 Eiichi Shoguchi,2 Tadasu Shin-i,9 Antoinetta Spagnuolo,18 Didier Stainier,22 Miho M. Suzuki,23 Olivier Tassy,11 Naohito Takatori,2 Miki Tokuoka,2 Kasumi Yagi,2 Fumiko Yoshizaki,13 Shuichi Wada,2 Cindy Zhang,1 P. Douglas Hyatt,24 Frank Larimer,24 Chris Detter,1 Norman Doggett,25 Tijana Glavina,1 Trevor Hawkins,1 Paul Richardson,1 Susan Lucas,1 Yuji Kohara,9dagger Michael Levine,726dagger Nori Satoh,2dagger Daniel S. Rokhsar1726dagger

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.

1 U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
2 Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
3 Marine Biological Laboratories, Woods Hole, MA 02543, USA.
4 Serono Reproductive Biology Institute, One Technology Place, Rockland, MA 02370, USA.
5 Department of Zoology and Entomology, University of Queensland, Brisbane, Qld 4072, Australia.
6 Department of Pathology, Stanford University School of Medicine, Stanford, CA 93950, USA.
7 Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA.
8 Montreal Neurological Institute, McGill University, Montreal, H3A 2T5, Canada.
9 National Institute of Genetics, Mishima 411-8540, Japan.
10 Bioinformatics Center, Institute for Chemical Research, Kyoto Univeristy, Uji, Kyoto 611-0011, Japan.
11 LGPD, IBDM, Case 907, Campus de Luminy, F-13288 Marseille Cedex 09, France.
12 Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.
13 Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan.
14 Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachiohji, Tokyo 192-0397, Japan.
15 Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
16 Drug Discovery Program, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.
17 Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
18 Stazione Zoologica "Anton Dohrn," Villa Comunale, 80121 Napoli, Italy.
19 IBM Watson Research Center, Post Office Box 218, Yorktown Heights, NY 10598, USA.
20 Asamushi Marine Biological Station, Graduate School of Science, Tohoku University, Asamushi, Aomori 039-3501, Japan.
21 University of Maryland, College Park, MD 20742, USA.
22 Department of Biochemistry and Biophysics, Programs in Developmental Biology, Genetics, and Human Genetics, University of California, San Francisco, CA 94143, USA.
23 Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
24 Oak Ridge National Laboratory, Post Office Box 2008, Oak Ridge, TN 37831, USA.
25 Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
26 Center for Integrative Genomics, University of California, Berkeley 94720, USA.
*   These authors contributed equally to this work.

dagger    To whom correspondence should be addressed. E-mail: ykohara{at}lab.nig.ac.jp (Y.K.), mlevine{at}uclink4.berkeley.edu (M.L.), satoh{at}ascidian.zool.kyoto-u.ac.jp (N.S.), dsrokhsar{at}lbl.gov (D.R.)

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A. Lomsadze, V. Ter-Hovhannisyan, Y. O. Chernoff, and M. Borodovsky (2005)
Nucleic Acids Res. 33, 6494-6506
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Vertebrate-Type Intron-Rich Genes in the Marine Annelid Platynereis dumerilii.
F. Raible, K. Tessmar-Raible, K. Osoegawa, P. Wincker, C. Jubin, G. Balavoine, D. Ferrier, V. Benes, P. de Jong, J. Weissenbach, et al. (2005)
Science 310, 1325-1326
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Double-Stranded RNA Induces Sequence-Specific Antiviral Silencing in Addition to Nonspecific Immunity in a Marine Shrimp: Convergence of RNA Interference and Innate Immunity in the Invertebrate Antiviral Response?.
J. Robalino, T. Bartlett, E. Shepard, S. Prior, G. Jaramillo, E. Scura, R. W. Chapman, P. S. Gross, C. L. Browdy, and G. W. Warr (2005)
J. Virol. 79, 13561-13571
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Molecular Phylogeny and Divergence Times of Deuterostome Animals.
J. E. Blair and S. B. Hedges (2005)
Mol. Biol. Evol. 22, 2275-2284
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Molecular signatures for sex in the Placozoa.
A. Y. Signorovitch, S. L. Dellaporta, and L. W. Buss (2005)
PNAS 102, 15518-15522
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Transposon-mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis.
Y. Sasakura, K. Nakashima, S. Awazu, T. Matsuoka, A. Nakayama, J.-i. Azuma, and N. Satoh (2005)
PNAS 102, 15134-15139
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Surfing with the tunicates into the post-genome era.
N. Satoh and M. Levine (2005)
Genes & Dev. 19, 2407-2411
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De novo discovery of a tissue-specific gene regulatory module in a chordate.
D. S. Johnson, Q. Zhou, K. Yagi, N. Satoh, W. Wong, and A. Sidow (2005)
Genome Res. 15, 1315-1324
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Tunicate Gonadotropin-Releasing Hormone (GnRH) Peptides Selectively Activate Ciona intestinalis GnRH Receptors and the Green Monkey Type II GnRH Receptor.
J. A. Tello, J. E. Rivier, and N. M. Sherwood (2005)
Endocrinology 146, 4061-4073
   Abstract »    Full Text »    PDF »


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