The amphioxus genome illuminates vertebrate origins and cephalochordate biology

被引：389

作者：

Holland, Linda Z. ^{[1
]}

Albalat, Ricard ^{[2
]}

Azumi, Kaoru ^{[3
]}

Benito-Gutierrez, Elia ^{[2
]}

Blow, Matthew J. ^{[4
]}

Bronner-Fraser, Marianne ^{[5
]}

Brunet, Frederic ^{[6
]}

Butts, Thomas ^{[7
]}

Candiani, Simona ^{[8
]}

Dishaw, Larry J. ^{[9
,10
]}

Ferrier, David E. K. ^{[7
,11
]}

Garcia-Fernandez, Jordi ^{[2
]}

Gibson-Brown, Jeremy J. ^{[12
,36
]}

Gissi, Carmela ^{[13
]}

Godzik, Adam ^{[14
]}

Hallbook, Finn ^{[15
]}

Hirose, Dan ^{[16
]}

Hosomichi, Kazuyoshi ^{[17
]}

Ikuta, Tetsuro

Inoko, Hidetoshi ^{[17
]}

Kasahara, Masanori ^{[18
]}

Kasamatsu, Jun ^{[18
]}

Kawashima, Takeshi ^{[19
]}

Kimura, Ayuko ^{[20
]}

Kobayashi, Masaaki

Kozmik, Zbynek ^{[21
]}

Kubokawa, Kaoru ^{[22
]}

Laudet, Vincent ^{[6
]}

Litman, Gary W. ^{[9
,10
,23
]}

McHardy, Alice C. ^{[24
]}

Meulemans, Daniel

Nonaka, Masaru ^{[20
]}

Olinski, Robert P. ^{[15
]}

Pancer, Zeev ^{[25
]}

Pennacchio, Len A. ^{[4
]}

Pestarino, Mario ^{[8
]}

Rast, Jonathan P. ^{[26
]}

Rigoutsos, Isidore ^{[24
]}

Robinson-Rechavi, Marc ^{[27
]}

Roch, Graeme ^{[28
]}

Saiga, Hidetoshi ^{[16
]}

Sasakura, Yasunori ^{[29
]}

Satake, Masanobu ^{[30
]}

Satou, Yutaka ^{[31
]}

Schubert, Michael ^{[6
]}

Sherwood, Nancy ^{[28
]}

Shiina, Takashi ^{[17
]}

Takatori, Naohito ^{[16
]}

Tello, Javier ^{[28
]}

Vopalensky, Pavel ^{[21
]}

机构：

[1] Univ Calif San Diego, Scripps Inst Oceanog, Div Marine Biol Res, La Jolla, CA 92093 USA

[2] Univ Barcelona, Fac Biol, Dept Genet, E-08028 Barcelona, Spain

[3] Hokkaido Univ, Div Innovat Res, Creat Res Initiat Sousei, Sapporo, Hokkaido 0010021, Japan

[4] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA

[5] CALTECH, Div Biol 139 74, Pasadena, CA 91125 USA

[6] Ecole Normale Super Lyon, CNRS, Inst Genom Fonct Lyon,UMR Biosci Lyon Gerland 524, UCBL,ENS,INRA 1288,IFR128, F-69364 Lyon 07, France

[7] Univ Oxford, Dept Zool, Oxford OX1 3PS, England

[8] Univ Genoa, Dipartimento Biol, I-16132 Genoa, Italy

[9] H Lee Moffitt Canc Ctr & Res Inst, Tampa, FL 33612 USA

[10] All Childrens Hosp, Dept Mol Genet, St Petersburg, FL 33701 USA

[11] Univ St Andrews, Gatty Marine Lab, St Andrews KY16 8LB, Fife, Scotland

[12] Washington Univ, Dept Biol, St Louis, MO 63130 USA

[13] Univ Milan, Dipartimento Sci Biomol Biotecnol, Milan, Italy

[14] Burnham Inst Med Res, La Jolla, CA 92037 USA

[15] Uppsala Univ, Dept Neurosci, Unit Dev Neurosci, Uppsala, Sweden

[16] Tokyo Metropolitan Univ, Grad Sch Sci & Engn, Dept Sci Biol, Tokyo 1920397, Japan

[17] Tokai Univ, Sch Med, Dept Mol Life Sci, Kanagawa 2591193, Japan

[18] Hokkaido Univ, Grad Sch Med, Dept Pathol, Sapporo, Hokkaido 0608638, Japan

[19] Univ Calif Berkeley, Ctr Integrat Genom, Dept Cell & Mol Biol, Berkeley, CA 94720 USA

[20] Univ Tokyo, Grad Sch Sci, Dept Biol Sci, Tokyo 113033, Japan

[21] Acad Sci Czech Republ, Inst Mol Genet, CR-14220 Prague 4, Czech Republic

[22] Univ Tokyo, Ocean Res Inst, Ctr Adv Marine Res, Tokyo 1648639, Japan

[23] Univ S Florida, Dept Pediat, St Petersburg, FL 33701 USA

[24] IBM Corp, Thomas J Watson Res Ctr, Bioinformat & Pattern Discovery Grp, Yorktown Hts, NY 10598 USA

[25] Univ Maryland, Inst Biotechnol, Ctr Marine Biotechnol, Baltimore, MD 21202 USA

[26] Univ Toronto, Sunnybrook Res Inst, Toronto, ON M4N 3M5, Canada

[27] Univ Toronto, Dept Med Biophys, Toronto, ON M4N 3M5, Canada

[28] Univ Lausanne, Dept Ecol & Evolut, CH-1015 Lausanne, Switzerland

[29] Univ Victoria, Dept Biol, Victoria, BC V8W 3N5, Canada

[30] Univ Tsukuba, Shimoda Marine Res Ctr, Shizuoka 4150025, Japan

[31] Tohoku Univ, Dept Mol Immunol, Inst Dev Aging & Canc, Sendai, Miyagi 9808575, Japan

[32] Kyoto Univ, Grad Sch Sci, Dept Zool, Kyoto 6068502, Japan

[33] Nagahama Inst Biosci & Technol, Fac Biosci, Dept Biosci, Shiga 5260829, Japan

[34] Sun Yat Sen Zhongshan Univ, Coll Life Sci, State Key Lab Biocontrol, Dept Biochem, Guangzhou, Guangdong, Peoples R China

[35] Juntendo Univ, Inst Environm & Gender Specif Med, Chiba 2790021, Japan

[36] Childrens Hosp, Oakland Res Inst, Oakland, CA 94609 USA

来源：

GENOME RESEARCH | 2008年 / 18卷 / 07期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

D O I：

10.1101/gr.073676.107

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates-a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.

引用

页码：1100 / 1111

页数：12

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