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Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation

Journal article
Authors Suda Parimala Ravindran
J. Luneburg
L. Gottschlich
V. Tams
M. Cordellier
Published in Scientific Reports
Volume 9
ISSN 2045-2322
Publication year 2019
Published at Department of marine sciences
Language en
Links dx.doi.org/10.1038/s41598-019-47226...
Keywords expression, genome, Science & Technology - Other Topics, ates of america, v110, p18753
Subject categories Biological Sciences

Abstract

Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or "hypothetical" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for "hypothetical proteins" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnia's genetic and phenotypic variability.

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