Ciona intestinalis v1.0
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Project Status

A draft of the Ciona intestinalis genome was generated using a whole genome shotgun strategy. The initial draft assembly and analysis of the euchromatic (gene-rich) portion o the genome appears in Science. The manuscript describes release version 1.0, a whole genome shotgun assembly of more than two million sequence fragments (a total of approximately 8.2X depth coverage from two haplotypes). BAC and cosmid libraries were end-sequenced to provide 0.2X coverage. The supporting data for this publication is currently available to download. Please check this page for future updates.

Assembly Releases

v2.0 (March 2005): The assembly release version 2.0 of the whole genome shotgun reads was constructed with the JAZZ assembler using paired end sequencing reads. Starting with a coverage of 11x, additional data--including BAC and FISH markers--were used to map scaffolds to chromosome arms. The current size of the assembly which includes unmapped scaffolds is 173Mb with 94Mb of the assembly mapped to chromosome arms.

v1.95 (October 2002): The assembly release version 1.95 of the whole genome shotgun reads was constructed with the JAZZ assembler, using paired end sequencing reads at a coverage of 11X. After trimming for vector and quality, 3.9 million reads assembled into 2242 scaffolds, totaling 117 Mb. Roughly half the genome is contained in 136 scaffolds at least 234 kb in length.

v1.0 (April 2002): This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired end sequencing reads at a coverage of 8.2X produced at the JGI. The assembly contains 116.7 million base pairs of nonrepetitive sequence in 2,501 scaffolds greater than 3 kb. Half of this (60 Mbp) is assembled into 117 scaffolds longer than 190 Kbp; 85% of the assembly (104.1 Mbp) is found in 905 scaffolds longer than 20 kb. Gene modeling and analysis were performed at the JGI.


US DOE Joint Genome Institute (Walnut Creek, CA, USA)
Department of Zoology, Graduate School of Science, Kyoto University (Kyoto, Japan)
Department of Molecular and Cellular Biology, University of California, Berkeley (Berkeley, CA, USA)
National Institute of Genetics (Mishima, Japan)
Oak Ridge National Laboratory (Oak Ridge, TN, USA)
Los Alamos National Laboratory (Los Alamos, NM, USA)

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

Future Plans

Deeper fosmid end-sequencing will provide additional long-range linking information and improved assemblies. Mapping efforts underway in Kyoto and elsewhere will ultimately allow mapping of the assembly to specific Ciona chromosomes. Regular updates of the assembly and gene models will be released.


This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.