The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins

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; Daniel S. Rokhsar

doi:10.1126/science.1080049

The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins

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 NeculaMasaru 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, Daniel S. Rokhsar

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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.

Original language	English (US)
Pages (from-to)	2157-2167
Number of pages	11
Journal	Science
Volume	298
Issue number	5601
DOIs	https://doi.org/10.1126/science.1080049
State	Published - Dec 13 2002
Externally published	Yes

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10.1126/science.1080049

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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., ... Rokhsar, D. S. (2002). The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science, 298(5601), 2157-2167. https://doi.org/10.1126/science.1080049

@article{1cf45c34466142a39bec16651b0f178c,

title = "The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins",

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.",

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

year = "2002",

month = dec,

day = "13",

doi = "10.1126/science.1080049",

language = "English (US)",

volume = "298",

pages = "2157--2167",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "5601",

}

Dehal, P, Satou, Y, Campbell, RK, Chapman, J, Degnan, B, De Tomaso, A, Davidson, B, Di Gregorio, A, Gelpke, M, Goodstein, DM, Harafuji, N, Hastings, KEM, Ho, I, Hotta, K, Huang, W, Kawashima, T, Lemaire, P, Martinez, D, Meinertzhagen, IA, Necula, S, Nonaka, M, Putnam, N, Rash, S, Saiga, H, Satake, M, Terry, A, Yamada, L, Wang, HG, Awazu, S, Azumi, K, Boore, J, Branno, M, Chin-bow, S, DeSantis, R, Doyle, S, Francino, P, Keys, DN, Haga, S, Hayashi, H, Hino, K, Imai, KS, Inaba, K, Kano, S, Kobayashi, K, Kobayashi, M, Lee, BI, Makabe, KW, 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, MM, Tassy, O, Takatori, N, Tokuoka, M, Yagi, K, Yoshizaki, F, Wada, S, Zhang, C, Hyatt, PD, Larimer, F, Detter, C, Doggett, N, Glavina, T, Hawkins, T, Richardson, P, Lucas, S, Kohara, Y, Levine, M, Satoh, N & Rokhsar, DS 2002, 'The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins', Science, vol. 298, no. 5601, pp. 2157-2167. https://doi.org/10.1126/science.1080049

TY - JOUR

T1 - The draft genome of Ciona intestinalis

T2 - Insights into chordate and vertebrate origins

AU - Dehal, Paramvir

AU - Satou, Yutaka

AU - Campbell, Robert K.

AU - Chapman, Jarrod

AU - Degnan, Bernard

AU - De Tomaso, Anthony

AU - Davidson, Brad

AU - Di Gregorio, Anna

AU - Gelpke, Maarten

AU - Goodstein, David M.

AU - Harafuji, Naoe

AU - Hastings, Kenneth E.M.

AU - Ho, Isaac

AU - Hotta, Kohji

AU - Huang, Wayne

AU - Kawashima, Takeshi

AU - Lemaire, Patrick

AU - Martinez, Diego

AU - Meinertzhagen, Ian A.

AU - Necula, Simona

AU - Nonaka, Masaru

AU - Putnam, Nik

AU - Rash, Sam

AU - Saiga, Hidetoshi

AU - Satake, Masanobu

AU - Terry, Astrid

AU - Yamada, Lixy

AU - Wang, Hong Gang

AU - Awazu, Satoko

AU - Azumi, Kaoru

AU - Boore, Jeffrey

AU - Branno, Margherita

AU - Chin-bow, Stephen

AU - DeSantis, Rosaria

AU - Doyle, Sharon

AU - Francino, Pilar

AU - Keys, David N.

AU - Haga, Shinobu

AU - Hayashi, Hiroko

AU - Hino, Kyosuke

AU - Imai, Kaoru S.

AU - Inaba, Kazuo

AU - Kano, Shungo

AU - Kobayashi, Kenji

AU - Kobayashi, Mari

AU - Lee, Byung In

AU - Makabe, Kazuhiro W.

AU - Manohar, Chitra

AU - Matassi, Giorgio

AU - Medina, Monica

AU - Mochizuki, Yasuaki

AU - Mount, Steve

AU - Morishita, Tomomi

AU - Miura, Sachiko

AU - Nakayama, Akie

AU - Nishizaka, Satoko

AU - Nomoto, Hisayo

AU - Ohta, Fumiko

AU - Oishi, Kazuko

AU - Rigoutsos, Isidore

AU - Sano, Masako

AU - Sasaki, Akane

AU - Sasakura, Yasunori

AU - Shoguchi, Eiichi

AU - Shin-i, Tadasu

AU - Spagnuolo, Antoinetta

AU - Stainier, Didier

AU - Suzuki, Miho M.

AU - Tassy, Olivier

AU - Takatori, Naohito

AU - Tokuoka, Miki

AU - Yagi, Kasumi

AU - Yoshizaki, Fumiko

AU - Wada, Shuichi

AU - Zhang, Cindy

AU - Hyatt, P. Douglas

AU - Larimer, Frank

AU - Detter, Chris

AU - Doggett, Norman

AU - Glavina, Tijana

AU - Hawkins, Trevor

AU - Richardson, Paul

AU - Lucas, Susan

AU - Kohara, Yuji

AU - Levine, Michael

AU - Satoh, Nori

AU - Rokhsar, Daniel S.

PY - 2002/12/13

Y1 - 2002/12/13

N2 - 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.

AB - 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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UR - http://www.scopus.com/inward/citedby.url?scp=2242464840&partnerID=8YFLogxK

U2 - 10.1126/science.1080049

DO - 10.1126/science.1080049

M3 - Article

C2 - 12481130

AN - SCOPUS:2242464840

SN - 0036-8075

VL - 298

SP - 2157

EP - 2167

JO - Science

JF - Science

IS - 5601

ER -

The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins

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