Web-based histology reference atlas for the freshwater crustacean Daphnia magna

Daphnia, an important model system for the study of evolution, development, phenotypic plasticity, and environmental health, lacks a modern reference atlas for microanatomy. To facilitate the comprehensive assessment of phenotypic effects of genes and environment, we created the Daphnia histology reference atlas (http://daphnia.io/anatomy/), a tractable, interactive web-based tool that provides insight into normal phenotype through vectorized annotations overlaid onto digital histology sections imaged at 40X magnification. Guided by our expert-curated and multimodal informed hierarchical anatomical ontology, we show that this resource can be used to elucidate sex-specific differences between female and male Daphnia magna in each of 3 orthogonal planes, providing new insight for the study of sex-specific traits. This atlas is a new, open-source resource for the Daphnia community to facilitate education and research collaboration, and as a precursor for the 3D atlas. It is also our intention that this atlas aids in phenotypic anchoring of large-scale biomolecular (multi-omics) data from comparative toxicological studies. Greater access to high-quality histological data may clarify cross-correlations between microanatomic and multi-omic phenotypes caused by genetic variation, environment, and disease across phylogeny.