The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

被引：449

作者：

Braasch, Ingo ^{[1
,34
]}

Gehrke, Andrew R. ^{[2
]}

Smith, Jeramiah J. ^{[3
]}

Kawasaki, Kazuhiko ^{[4
]}

Manousaki, Tereza ^{[5
]}

Pasquier, Jeremy ^{[6
]}

Amores, Angel ^{[1
]}

Desvignes, Thomas ^{[1
]}

Batzel, Peter ^{[1
]}

Catchen, Julian ^{[7
]}

Berlin, Aaron M. ^{[8
]}

Campbell, Michael S. ^{[9
,35
]}

Barrell, Daniel ^{[10
,11
]}

Martin, Kyle J. ^{[12
,36
]}

Mulley, John F. ^{[13
]}

Ravi, Vydianathan ^{[14
]}

Lee, Alison P. ^{[14
]}

Nakamura, Tetsuya ^{[2
]}

Chalopin, Domitille ^{[15
,37
]}

Fan, Shaohua ^{[16
,38
]}

Wcisel, Dustin ^{[17
,18
]}

Canestro, Cristian ^{[19
,20
]}

Sydes, Jason ^{[1
]}

Beaudry, Felix E. G. ^{[21
]}

Sun, Yi ^{[22
,23
]}

Hertel, Jana ^{[24
,39
]}

Beam, Michael J. ^{[1
]}

Fasold, Mario ^{[24
,40
]}

Ishiyama, Mikio ^{[25
]}

Johnson, Jeremy ^{[8
]}

Kehr, Steffi ^{[24
]}

Lara, Marcia ^{[8
]}

Letaw, John H. ^{[1
]}

Litman, Gary W. ^{[26
]}

Litman, Ronda T. ^{[26
]}

Mikami, Masato ^{[27
]}

Ota, Tatsuya ^{[28
]}

Saha, Nil Ratan ^{[29
]}

Williams, Louise ^{[8
]}

Stadler, Peter F. ^{[24
]}

Wang, Han ^{[22
,23
]}

Taylor, John S. ^{[21
]}

Fontenot, Quenton ^{[30
]}

Ferrara, Allyse ^{[30
]}

Searle, Stephen M. J. ^{[10
]}

Aken, Bronwen ^{[10
,11
]}

Yandell, Mark ^{[9
]}

Schneider, Igor ^{[31
]}

Yoder, Jeffrey A. ^{[17
,18
]}

Volff, Jean-Nicolas ^{[15
]}

机构：

[1] Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA

[2] Univ Chicago, Dept Organismal Biol & Anat, 1025 E 57Th St, Chicago, IL 60637 USA

[3] Univ Kentucky, Dept Biol, Lexington, KY USA

[4] Penn State Univ, Dept Anthropol, University Pk, PA 16802 USA

[5] Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture, Iraklion, Greece

[6] INRA, LPGP, UR1037, Campus Beaulieu, F-35042 Rennes, France

[7] Univ Illinois, Dept Anim Biol, Urbana, IL 61801 USA

[8] Broad Inst MIT & Harvard, Cambridge, MA USA

[9] Univ Utah, Eccles Inst Human Genet, Salt Lake City, UT USA

[10] Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Hinxton, England

[11] European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Hinxton, England

[12] Univ Oxford, Dept Zool, Oxford, England

[13] Bangor Univ, Sch Biol Sci, Bangor, Gwynedd, Wales

[14] ASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore, Singapore

[15] Ecole Normale Super Lyon, Inst Genom Fonct Lyon, F-69364 Lyon, France

[16] Univ Konstanz, Dept Biol, Constance, Germany

[17] N Carolina State Univ, Dept Mol Biomed Sci, Raleigh, NC 27695 USA

[18] N Carolina State Univ, Ctr Comparat Med & Translat Res, Raleigh, NC 27695 USA

[19] Univ Barcelona, Dept Genet, Barcelona, Spain

[20] Univ Barcelona, Inst Recerca Biodiversitat, Barcelona, Spain

[21] Univ Victoria, Dept Biol, POB 1700, Victoria, BC V8W 2Y2, Canada

[22] Soochow Univ, Ctr Circadian Clocks, Suzhou, Peoples R China

[23] Soochow Univ, Coll Med, Sch Biol & Basic Med Sci, Suzhou, Peoples R China

[24] Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany

[25] Nippon Dent Univ Coll Niigata, Dept Dent Hyg, Niigata, Japan

[26] Univ S Florida, Morsani Coll Med, Dept Pediat, St Petersburg, FL 33701 USA

[27] Nippon Dent Univ, Sch Life Dent Niigata, Dept Microbiol, Niigata, Japan

[28] SOKENDAI Grad Univ Adv Studies, Dept Evolutionary Studies Biosyst, Hayama, Japan

[29] Benaroya Res Inst, Mol Genet Program, Seattle, WA USA

[30] Nicholls State Univ, Dept Biol Sci, Thibodaux, LA 70310 USA

[31] Fed Univ Para, Inst Ciencias Biol, BR-66059 Belem, Para, Brazil

[32] Univ Konstanz, Int Max Planck Res Sch Organismal Biol, Constance, Germany

[33] Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, Uppsala, Sweden

[34] Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA

[35] Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA

[36] Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England

[37] Univ Georgia, Dept Genet, Athens, GA 30602 USA

[38] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA

[39] UFZ Helmholtz Ctr Environm Res, Young Investigators Grp Bioinformat & Transcript, Leipzig, Germany

[40] ecSeq Bioinformat, Leipzig, Germany

[41] Genome Anal Ctr, Vertebrate & Hlth Genom, Norwich, Norfolk, England

来源：

NATURE GENETICS | 2016年 / 48卷 / 04期

基金：

美国国家卫生研究院; 欧洲研究理事会; 英国生物技术与生命科学研究理事会; 中国国家自然科学基金; 美国国家科学基金会; 日本学术振兴会; 英国惠康基金;

关键词：

RAY-FINNED FISH; MHC CLASS-I; COMPLEX-CLASS-I; COMPREHENSIVE ANALYSIS; PROVIDES INSIGHTS; GENE DUPLICATION; HOX GENES; ROUNDS; ZEBRAFISH; COELACANTH;

D O I：

10.1038/ng.3526

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

引用

页码：427 / +

页数：13

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