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The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins
Paramvir Dehal,1*Yutaka Satou,2*Robert K. Campbell,34Jarrod Chapman,1Bernard Degnan,5Anthony De Tomaso,6Brad Davidson,7Anna Di Gregorio,7Maarten Gelpke,1David M. Goodstein,1Naoe Harafuji,7Kenneth E. M. Hastings,8Isaac Ho,1Kohji Hotta,9Wayne Huang,1Takeshi Kawashima,10Patrick Lemaire,11Diego Martinez,1Ian A. Meinertzhagen,12Simona Necula,1Masaru Nonaka,13Nik Putnam,1Sam Rash,1Hidetoshi Saiga,14Masanobu Satake,15Astrid Terry,1Lixy Yamada,2Hong-Gang Wang,16Satoko Awazu,2Kaoru Azumi,17Jeffrey Boore,1Margherita Branno,18Stephen Chin-bow,19Rosaria DeSantis,18Sharon Doyle,1Pilar Francino,1David N. Keys,17Shinobu Haga,9Hiroko Hayashi,9Kyosuke Hino,2Kaoru S. Imai,2Kazuo Inaba,20Shungo Kano,218Kenji Kobayashi,2Mari Kobayashi,2Byung-In Lee,1Kazuhiro W. Makabe,2Chitra Manohar,1Giorgio Matassi,18Monica Medina,1Yasuaki Mochizuki,2Steve Mount,21Tomomi Morishita,9Sachiko Miura,9Akie Nakayama,2Satoko Nishizaka,9Hisayo Nomoto,9Fumiko Ohta,9Kazuko Oishi,9Isidore Rigoutsos,19Masako Sano,9Akane Sasaki,2Yasunori Sasakura,2Eiichi Shoguchi,2Tadasu Shin-i,9Antoinetta Spagnuolo,18Didier Stainier,22Miho M. Suzuki,23Olivier Tassy,11Naohito Takatori,2Miki Tokuoka,2Kasumi Yagi,2Fumiko Yoshizaki,13Shuichi Wada,2Cindy Zhang,1P. Douglas Hyatt,24Frank Larimer,24Chris Detter,1Norman Doggett,25Tijana Glavina,1Trevor Hawkins,1Paul Richardson,1Susan Lucas,1Yuji Kohara,9Michael Levine,726Nori Satoh,2Daniel S. Rokhsar1726
The first chordates appear in the fossil record at the time of the
Cambrian explosion, nearly 550 million years ago. The modernascidian
tadpole represents a plausible approximation to theseancestral
chordates. To illuminate the origins of chordate andvertebrates, we
generated a draft of the protein-coding portionof the genome of the
most studied ascidian, Ciona intestinalis.The
Ciona genome contains ~16,000 protein-coding genes,
similarto the number in other invertebrates, but only half that foundin vertebrates. Vertebrate gene families are typically found insimplified form in Ciona, suggesting that ascidians contain
thebasic ancestral complement of genes involved in cell signalingand
development. The ascidian genome has also acquired a numberof
lineage-specific innovations, including a group of genes engagedin
cellulose metabolism that are related to those in bacteriaand 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.
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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