Evolutionary Analysis of Gene-expression Localization in the Model Crustacean, Daphnia pulex

Whole-genome sequencing provides lists of genes of putative relevance to organismal biology. However, in all metazoans, a large fraction of inferred genes has no known functions, in some cases with no orthologs in related species, and even orthology at the DNA-sequence level often not providing indisputable evidence of gene function. A first step towards resolving the functional features of gene encyclopedias in multicellular species is to evaluate the tissues in which individual genes are expressed. Here, we report on assays of expression for the full sets of protein-coding and long-noncoding RNA (lncRNA) genes across eight tissues of the microcrustacean Daphnia pulex. We also take advantage of a large database on levels of polymorphism and divergence for each gene to infer various features of selection operating on genes expressed in different tissues, including novel genes restricted to particular Daphnia lineages. In addition to generating a resource for future work on the molecular, cellular, and developmental biology of the model species D. pulex, this study highlights a number of novel findings. These include the identification of sets of genes experiencing unusual forms of positive selection, the discovery of unusual patterns of evolution in the pool of testes-specific genes, rapid turnover and sequence evolution of lncRNA genes, and the pervasive operation of selection on genes thought to be D. pulex-specific.