The Ecoresponsive Genome of Daphnia pulex

被引：960

作者：

Colbourne, John K. ^{[1
]}

Pfrender, Michael E. ^{[2
]}

Gilbert, Donald ^{[1
,3
]}

Thomas, W. Kelley ^{[4
]}

Tucker, Abraham ^{[3
,4
]}

Oakley, Todd H. ^{[5
]}

Tokishita, Shinichi ^{[6
]}

Aerts, Andrea ^{[7
]}

Arnold, Georg J. ^{[8
]}

Basu, Malay Kumar ^{[9
]}

Bauer, Darren J. ^{[4
]}

Caceres, Carla E. ^{[10
]}

Carmel, Liran ^{[9
]}

Casola, Claudio ^{[3
]}

Choi, Jeong-Hyeon ^{[1
]}

Detter, John C. ^{[7
]}

Dong, Qunfeng ^{[1
]}

Dusheyko, Serge ^{[7
]}

Eads, Brian D. ^{[1
,3
]}

Froehlich, Thomas ^{[8
]}

Geiler-Samerotte, Kerry A. ^{[5
]}

Gerlach, Daniel ^{[11
,12
]}

Hatcher, Phil ^{[4
]}

Jogdeo, Sanjuro ^{[4
]}

Krijgsveld, Jeroen ^{[13
,14
,15
]}

Kriventseva, Evgenia V. ^{[11
,12
]}

Kueltz, Dietmar ^{[16
]}

Laforsch, Christian ^{[17
,18
]}

Lindquist, Erika ^{[7
]}

Lopez, Jacqueline ^{[1
]}

Manak, J. Robert ^{[19
]}

Muller, Jean ^{[20
]}

Pangilinan, Jasmyn ^{[7
]}

Patwardhan, Rupali P. ^{[1
]}

Pitluck, Samuel ^{[7
]}

Pritham, Ellen J. ^{[21
]}

Rechtsteiner, Andreas ^{[1
]}

Rho, Mina ^{[22
]}

Rogozin, Igor B. ^{[9
]}

Sakarya, Onur ^{[5
]}

Salamov, Asaf ^{[7
]}

Schaack, Sarah ^{[3
,21
]}

Shapiro, Harris ^{[7
]}

Shiga, Yasuhiro ^{[6
]}

Skalitzky, Courtney ^{[19
]}

Smith, Zachary ^{[1
]}

Souvorov, Alexander ^{[9
]}

Sung, Way ^{[4
]}

Tang, Zuojian ^{[1
]}

Tsuchiya, Dai ^{[1
]}

机构：

[1] Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN 47405 USA

[2] Utah State Univ, Dept Biol, Logan, UT 84322 USA

[3] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

[4] Univ New Hampshire, Hubbard Ctr Genome Studies, Durham, NH 03824 USA

[5] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA

[6] Tokyo Univ Pharm & Life Sci, Sch Life Sci, Div Environm Sci, Lab Environm & Mol Biol, Tokyo 1920392, Japan

[7] JGI, Dept Energy, Walnut Creek, CA 94598 USA

[8] Univ Munich, Gene Ctr, Lab Funct Genome Anal LAFUGA, D-82152 Planegg Martinsried, Germany

[9] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA

[10] Univ Illinois, Sch Integrat Biol, Urbana, IL 61801 USA

[11] Univ Geneva, Sch Med, CH-1211 Geneva, Switzerland

[12] Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland

[13] Univ Utrecht, Bijvoet Ctr Biomol Res, Biomol Mass Spectrometry & Prote Grp, NL-3584 CA Utrecht, Netherlands

[14] Univ Utrecht, Utrecht Inst Pharmaceut Sci, NL-3584 CA Utrecht, Netherlands

[15] Univ Utrecht, Netherlands Prote Ctr, NL-3584 CA Utrecht, Netherlands

[16] Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA

[17] Univ Munich, Dept Biol 2, D-82152 Planegg Martinsried, Germany

[18] Univ Munich, GeoBio Ctr Munich, D-82152 Planegg Martinsried, Germany

[19] Roche NimbleGen Inc, Gene Express, Madison, WI 53719 USA

[20] European Mol Biol Lab, Struct & Computat Biol Unit, D-69117 Heidelberg, Germany

[21] Univ Texas Arlington, Dept Biol, Arlington, TX 76019 USA

[22] Indiana Univ, Sch Informat & Comp, Bloomington, IN 47408 USA

[23] Indiana Univ, Sch Publ & Environm Affairs, Bloomington, IN 47405 USA

[24] Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada

[25] Univ Illinois, Dept Entomol, Urbana, IL 61801 USA

[26] Univ London Imperial Coll Sci Technol & Med, London SW7 2AZ, England

[27] Genome Project Solut, Hercules, CA 94547 USA

[28] Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA

来源：

SCIENCE | 2011年 / 331卷 / 6017期

基金：

美国国家科学基金会;

关键词：

CAENORHABDITIS-ELEGANS; GENES; EXPRESSION; DUPLICATIONS; EVOLUTION; MAGNA;

D O I：

10.1126/science.1197761

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：

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

引用

页码：555 / 561

页数：7

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