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, 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, Science 331 (6017) :555-61 (2011).
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DOI
10.1126/science.1197761
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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.