Hydra AEP Genome Project Portal

The simple freshwater cnidarian polyps belonging to the genus Hydra are among the longest-studied and best-characterized cnidarian research organisms, with the first experiments in Hydra dating back to the 1700s. Hydra are notable for their exceptional resilience, exhibiting negligible senescence and a nearly limitless regenerative capacity. Hydra are also relatively simple, possessing only a single life cycle stage and a small number of well-defined cell types. These features, along with Cnidaria's phylogenetic position as sister to Bilateria, makes Hydra a powerful system to study fundamental biological principles including those related to patterning, stem cell biology, aging, and regeneration.

The advent of powerful tools and resources — including a reference genome, a single-cell gene expression atlas, knock-down techniques, and transgenesis — has enabled Hydra researchers to explore topics such as regeneration and patterning at the molecular level. However, complicating the effective use of these tools is the fact that these resources were developed using different genetic backgrounds. Specifically, the original reference genome was generated using strain 105 of Hydra vulgaris, formerly H. magnipapillata, whereas all transgenic Hydra lines and the single-cell expression atlas were generated using the AEP strain.

To provide a genomic resource better suited for strain AEP-derived genomic and transcriptomic data, and to better enable comparative molecular research in cnidarians, we sequenced, assembled, and annotated a chromosome-level assembly for the AEP strain of H. vulgaris. In addition, we generated and annotated a draft genome assembly for another brown Hydra species, H. oligactis.

This genome portal is intended to provide genomic and transcriptomic resources for researchers interested in Hydra molecular biology. These include browsers for the strain AEP H. vulgaris and H. oligactis genome assemblies and an interactive interface for interrogating the H. vulgaris single-cell gene expression atlas. We also provide functional annotation data for the strain AEP genome gene models, including protein domain composition and orthology predictions. Finally, we provide data on chromatin accessibility, histone modifications, and sequence conservation that shed light on the Hydra cis-regulatory landscape.