The Ecoresponsive Genome of Daphnia pulex
By J. Colbourne, M. Pfrender, D. Gilbert, W. Thomas, Abraham E. Tucker, Todd H. Oakley, S. Tokishita, A. Aerts, G. Arnold, Malay Kumar Basu and 59 more. Science, 2011
1,240 citations recorded by the source corpus.
The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions. 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.
Subfields: Environmental Chemistry, Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/ff7d9fdf8785dd360129482568661227b7fa58e6
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In Environmental Chemistry
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Citations in the corpus
- The evolutionary origin of orphan genes (2011, background): “A function of orphan gene families in responding to environmental stimuli was suggested for the water flea Daphnia pulex , a model organism for ecological researc”
- The Genome Portal of the Department of Energy Joint Genome Institute (2011, background): “In addition to plants and fungi, diverse eukaryotes from Amoebozoa (4), Metazoa (5), Choanozoa (6), Heterobosea (7), Heterokonta (8–10), Rhizaria, Haptophyta and Cryptophyta can be analyzed with a collection of tools linked directly to their genome databases.”
- Net effects of multiple stressors in freshwater ecosystems: a meta‐analysis (2016, background): “…water fleas (Daphnia © 2015 John Wiley & Sons Ltd, Global Change Biology, 22, 180–189 spp.) that are often focal species in lakes and ponds have been shown to be highly responsive (Colbourne et al., 2011) and capable of rapidly evolving in the face of environmental change (De Meester et al., 2011).”
- Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, background): “1, last accessed November 19, 2013; Colbourne et al. 2011).”