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The ecoresponsive genome of Daphnia pulex.

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.

Pubmed ID: 21292972


  • 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 JH
  • 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


Science (New York, N.Y.)

Publication Data

February 4, 2011

Associated Grants

  • Agency: NIEHS NIH HHS, Id: P42 ES004699
  • Agency: NIEHS NIH HHS, Id: P42 ES004699-25
  • Agency: NIEHS NIH HHS, Id: P42ES004699
  • Agency: NIEHS NIH HHS, Id: R01 ES019324
  • Agency: NIGMS NIH HHS, Id: R24 GM078274
  • Agency: NIGMS NIH HHS, Id: R24 GM078274-01A1
  • Agency: NIGMS NIH HHS, Id: R24GM07827401
  • Agency: Intramural NIH HHS, Id:

Mesh Terms

  • Adaptation, Physiological
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Chromosome Mapping
  • Daphnia
  • Ecosystem
  • Environment
  • Evolution, Molecular
  • Gene Conversion
  • Gene Duplication
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Genes
  • Genes, Duplicate
  • Genome
  • Metabolic Networks and Pathways
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Multigene Family
  • Phylogeny
  • Sequence Analysis, DNA