The ecoresponsive genome of Daphnia pulex

John K. Colbourne, Michael E. Pfrender, Donald Gilbert, W. Kelley Thomas, Abraham Tucker, Todd H. Oakley, Shinichi Tokishita, Andrea Aerts, Georg J. Arnold, Malay Kumar Basu, Darren J. Bauer, Carla E. Cáceres, Liran Carmel, Claudio Casola, Jeong-Hyeon Choi, John C. Detter, Qunfeng Dong, Serge Dusheyko, Brian D. Eads, Thomas Fröhlich & 49 others Kerry A. Geiler-Samerotte, Daniel Gerlach, Phil Hatcher, Sanjuro Jogdeo, Jeroen Krijgsveld, Evgenia V. Kriventseva, Dietmar Kültz, Christian Laforsch, Erika Lindquist, Jacqueline Lopez, J. Robert Manak, Jean Muller, Jasmyn Pangilinan, Rupali P. Patwardhan, Samuel Pitluck, Ellen J. Pritham, Andreas Rechtsteiner, Mina Rho, Igor B. Rogozin, Onur Sakarya, Asaf Salamov, Sarah Schaack, Harris Shapiro, Yasuhiro Shiga, Courtney Skalitzky, Zachary Smith, Alexander Souvorov, Way Sung, Zuojian Tang, Dai Tsuchiya, Hank Tu, Harmjan Vos, Mei Wang, Yuri I. Wolf, Hideo Yamagata, Takuji Yamada, Yuzhen Ye, Joseph R. Shaw, Justen Andrews, Teresa J. Crease, Haixu Tang, Susan M. Lucas, Hugh M. Robertson, Peer Bork, Eugene V. Koonin, Evgeny M. Zdobnov, Igor V. Grigoriev, Michael Lynch, Jeffrey L. Boore

Research output: Contribution to journalArticle

736 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)555-561
Number of pages7
JournalScience
Volume331
Issue number6017
DOIs
StatePublished - Feb 4 2011

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Daphnia
Genome
Genes
Gene Duplication
Proteome
Multigene Family
Metabolic Networks and Pathways
Maintenance
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Colbourne, J. K., Pfrender, M. E., Gilbert, D., Thomas, W. K., Tucker, A., Oakley, T. H., ... Boore, J. L. (2011). The ecoresponsive genome of Daphnia pulex. Science, 331(6017), 555-561. https://doi.org/10.1126/science.1197761

The ecoresponsive genome of Daphnia pulex. / Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Cáceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Fröhlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V.; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, J. Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

In: Science, Vol. 331, No. 6017, 04.02.2011, p. 555-561.

Research output: Contribution to journalArticle

Colbourne, JK, Pfrender, ME, Gilbert, D, Thomas, WK, Tucker, A, Oakley, TH, Tokishita, S, Aerts, A, Arnold, GJ, Basu, MK, Bauer, DJ, Cáceres, CE, Carmel, L, Casola, C, Choi, J-H, Detter, JC, Dong, Q, Dusheyko, S, Eads, BD, Fröhlich, T, Geiler-Samerotte, KA, Gerlach, D, Hatcher, P, Jogdeo, S, Krijgsveld, J, Kriventseva, EV, Kültz, D, Laforsch, C, Lindquist, E, Lopez, J, Manak, JR, Muller, J, Pangilinan, J, Patwardhan, RP, Pitluck, S, Pritham, EJ, Rechtsteiner, A, Rho, M, Rogozin, IB, Sakarya, O, Salamov, A, Schaack, S, Shapiro, H, Shiga, Y, Skalitzky, C, Smith, Z, Souvorov, A, Sung, W, Tang, Z, Tsuchiya, D, Tu, H, Vos, H, Wang, M, Wolf, YI, Yamagata, H, Yamada, T, Ye, Y, Shaw, JR, Andrews, J, Crease, TJ, Tang, H, Lucas, SM, Robertson, HM, Bork, P, Koonin, EV, Zdobnov, EM, Grigoriev, IV, Lynch, M & Boore, JL 2011, 'The ecoresponsive genome of Daphnia pulex', Science, vol. 331, no. 6017, pp. 555-561. https://doi.org/10.1126/science.1197761
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH et al. The ecoresponsive genome of Daphnia pulex. Science. 2011 Feb 4;331(6017):555-561. https://doi.org/10.1126/science.1197761
Colbourne, John K. ; Pfrender, Michael E. ; Gilbert, Donald ; Thomas, W. Kelley ; Tucker, Abraham ; Oakley, Todd H. ; Tokishita, Shinichi ; Aerts, Andrea ; Arnold, Georg J. ; Basu, Malay Kumar ; Bauer, Darren J. ; Cáceres, Carla E. ; Carmel, Liran ; Casola, Claudio ; Choi, Jeong-Hyeon ; Detter, John C. ; Dong, Qunfeng ; Dusheyko, Serge ; Eads, Brian D. ; Fröhlich, Thomas ; Geiler-Samerotte, Kerry A. ; Gerlach, Daniel ; Hatcher, Phil ; Jogdeo, Sanjuro ; Krijgsveld, Jeroen ; Kriventseva, Evgenia V. ; Kültz, Dietmar ; Laforsch, Christian ; Lindquist, Erika ; Lopez, Jacqueline ; Manak, J. Robert ; Muller, Jean ; Pangilinan, Jasmyn ; Patwardhan, Rupali P. ; Pitluck, Samuel ; Pritham, Ellen J. ; Rechtsteiner, Andreas ; Rho, Mina ; Rogozin, Igor B. ; Sakarya, Onur ; Salamov, Asaf ; Schaack, Sarah ; Shapiro, Harris ; Shiga, Yasuhiro ; Skalitzky, Courtney ; Smith, Zachary ; Souvorov, Alexander ; Sung, Way ; Tang, Zuojian ; Tsuchiya, Dai ; Tu, Hank ; Vos, Harmjan ; Wang, Mei ; Wolf, Yuri I. ; Yamagata, Hideo ; Yamada, Takuji ; Ye, Yuzhen ; Shaw, Joseph R. ; Andrews, Justen ; Crease, Teresa J. ; Tang, Haixu ; Lucas, Susan M. ; Robertson, Hugh M. ; Bork, Peer ; Koonin, Eugene V. ; Zdobnov, Evgeny M. ; Grigoriev, Igor V. ; Lynch, Michael ; Boore, Jeffrey L. / The ecoresponsive genome of Daphnia pulex. In: Science. 2011 ; Vol. 331, No. 6017. pp. 555-561.
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abstract = "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.",
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AU - Pfrender, Michael E.

AU - Gilbert, Donald

AU - Thomas, W. Kelley

AU - Tucker, Abraham

AU - Oakley, Todd H.

AU - Tokishita, Shinichi

AU - Aerts, Andrea

AU - Arnold, Georg J.

AU - Basu, Malay Kumar

AU - Bauer, Darren J.

AU - Cáceres, Carla E.

AU - Carmel, Liran

AU - Casola, Claudio

AU - Choi, Jeong-Hyeon

AU - Detter, John C.

AU - Dong, Qunfeng

AU - Dusheyko, Serge

AU - Eads, Brian D.

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AU - Geiler-Samerotte, Kerry A.

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AU - Hatcher, Phil

AU - Jogdeo, Sanjuro

AU - Krijgsveld, Jeroen

AU - Kriventseva, Evgenia V.

AU - Kültz, Dietmar

AU - Laforsch, Christian

AU - Lindquist, Erika

AU - Lopez, Jacqueline

AU - Manak, J. Robert

AU - Muller, Jean

AU - Pangilinan, Jasmyn

AU - Patwardhan, Rupali P.

AU - Pitluck, Samuel

AU - Pritham, Ellen J.

AU - Rechtsteiner, Andreas

AU - Rho, Mina

AU - Rogozin, Igor B.

AU - Sakarya, Onur

AU - Salamov, Asaf

AU - Schaack, Sarah

AU - Shapiro, Harris

AU - Shiga, Yasuhiro

AU - Skalitzky, Courtney

AU - Smith, Zachary

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AU - Koonin, Eugene V.

AU - Zdobnov, Evgeny M.

AU - Grigoriev, Igor V.

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