The amphioxus genome and the evolution of the chordate karyotype

被引：1212

作者：

Putnam, Nicholas H. ^{[1
,2
]}

Butts, Thomas ^{[3
]}

Ferrier, David E. K. ^{[4
]}

Furlong, Rebecca F. ^{[3
]}

Hellsten, Uffe ^{[1
]}

Kawashima, Takeshi ^{[2
]}

Robinson-Rechavi, Marc ^{[5
,6
]}

Shoguchi, Eiichi ^{[7
]}

Terry, Astrid ^{[1
]}

Yu, Jr-Kai ^{[8
]}

Benito-Gutierrez, Elia ^{[9
]}

Dubchak, Inna ^{[1
]}

Garcia-Fernandez, Jordi ^{[10
]}

Gibson-Brown, Jeremy J. ^{[11
]}

Grigoriev, Igor V. ^{[1
]}

Horton, Amy C. ^{[11
]}

de Jong, Pieter J. ^{[12
]}

Jurka, Jerzy ^{[13
]}

Kapitonov, Vladimir V. ^{[13
]}

Kohara, Yuji ^{[14
]}

Kuroki, Yoko ^{[15
]}

Lindquist, Erika ^{[1
]}

Lucas, Susan ^{[1
]}

Osoegawa, Kazutoyo ^{[12
]}

Pennacchio, Len A. ^{[1
]}

Salamov, Asaf A. ^{[1
]}

Satou, Yutaka ^{[7
]}

Sauka-Spengler, Tatjana ^{[8
]}

Schmutz, Jeremy ^{[16
]}

Shin-I, Tadasu ^{[14
]}

Toyoda, Atsushi ^{[15
]}

Bronner-Fraser, Marianne ^{[8
]}

Fujiyama, Asao ^{[15
,17
]}

Holland, Linda Z. ^{[3
]}

Holland, Peter W. H. ^{[18
]}

Satoh, Nori ^{[7
]}

Rokhsar, Daniel S. ^{[1
,2
]}

机构：

[1] Dept Energy Joint Genome Inst, Walnut Creek, CA 94598 USA

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

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

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

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

[6] Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[7] Kyoto Univ, Dept Zool, Grad Sch Sci, Sakyo Ku, Kyoto 6068502, Japan

[8] CALTECH, Div Biol, Pasadena, CA 91125 USA

[9] Natl Inst Med Res, London NW7 1AA, England

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

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

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

[13] Genet Informat Res Inst, Mountain View, CA 94043 USA

[14] Natl Inst Genet, Mishima, Shizuoka 4118540, Japan

[15] RIKEN, Genom Sci Ctr, Tsurumi Ku, Kanagawa 2300045, Japan

[16] JGI Stanford Human Genome Ctr, Palo Alto, CA 94304 USA

[17] Res Org Informat & Syst, Natl Inst Informat, Chiyoda Ku, Tokyo 1018430, Japan

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

来源：

NATURE | 2008年 / 453卷 / 7198期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会;

关键词：

D O I：

10.1038/nature06967

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic similar to 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

引用

页码：1064 / U3

页数：9

共 81 条

[1] Evidence of en bloc duplication in vertebrate genomes [J].

Abi-Rached, L ;

Gilles, A ;

Shiina, T ;

Pontarotti, P ;

Inoko, H .

NATURE GENETICS, 2002, 31 (01) :100-105

[2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[3] Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes [J].

Aparicio, S ;

Chapman, J ;

Stupka, E ;

Putnam, N ;

Chia, J ;

Dehal, P ;

Christoffels, A ;

Rash, S ;

Hoon, S ;

Smit, A ;

Gelpke, MDS ;

Roach, J ;

Oh, T ;

Ho, IY ;

Wong, M ;

Detter, C ;

Verhoef, F ;

Predki, P ;

Tay, A ;

Lucas, S ;

Richardson, P ;

Smith, SF ;

Clark, MS ;

Edwards, YJK ;

Doggett, N ;

Zharkikh, A ;

Tavtigian, SV ;

Pruss, D ;

Barnstead, M ;

Evans, C ;

Baden, H ;

Powell, J ;

Glusman, G ;

Rowen, L ;

Hood, L ;

Tan, YH ;

Elgar, G ;

Hawkins, T ;

Venkatesh, B ;

Rokhsar, D ;

Brenner, S .

SCIENCE, 2002, 297 (5585) :1301-1310

[4] Molecular phylogeny and divergence times of deuterostome animals [J].

Blair, JE ;

Hedges, SB .

MOLECULAR BIOLOGY AND EVOLUTION, 2005, 22 (11) :2275-2284

[5] The gain and loss of genes during 600 million years of vertebrate evolution [J].

Blomme, Tine ;

Vandepoele, Klaas ;

De Bodt, Stefanie ;

Simillion, Cedric ;

Maere, Steven ;

Van de Peer, Yves .

GENOME BIOLOGY, 2006, 7 (05)

[6] Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida [J].

Bourlat, Sarah J. ;

Juliusdottir, Thorhildur ;

Lowe, Christopher J. ;

Freeman, Robert ;

Aronowicz, Jochanan ;

Kirschner, Mark ;

Lander, Eric S. ;

Thorndyke, Michael ;

Nakano, Hiroaki ;

Kohn, Andrea B. ;

Heyland, Andreas ;

Moroz, Leonid L. ;

Copley, Richard R. ;

Telford, Maximilian J. .

NATURE, 2006, 444 (7115) :85-88

[7] Majority of divergence between closely related DNA samples is due to indels [J].

Britten, RJ ;

Rowen, L ;

Williams, J ;

Cameron, RA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (08) :4661-4665

[8] Gene loss and evolutionary rates following whole-genome duplication in teleost fishes [J].

Brunet, Frederic G. ;

Roest Crollius, Hugues ;

Paris, Mathilde ;

Aury, Jean-Marc ;

Gibert, Patricia ;

Jaillon, Olivier ;

Laudet, Vincent ;

Robinson-Rechavi, Marc .

MOLECULAR BIOLOGY AND EVOLUTION, 2006, 23 (09) :1808-1816

[9] Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla [J].

Cameron, CB ;

Garey, JR ;

Swalla, BJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (09) :4469-4474

[10] Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis [J].

Castresana, J .

MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) :540-552

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