About the Hydra AEP Genome Project

The AEP strain of H. vulgaris was generated from a cross between the PA1 strain isolated by Dr. Carolyn Teragawa from a pond on the Haverford College campus near Philadelphia, Pennsylvania and the CA7 strain isolated by Drs. Lynne Littlefield and Carolyn Teragawa at Boulder Creek, near Susanville, California. The DNA used for genome sequencing was isolated from a clonally propagated population obtained from the laboratory of Thomas Bosch that was generated from an F1 self-cross of the original AEP strain.

The AEP assembly was generated using Oxford Nanopore (42x coverage), PacBio (5x coverage), 10X Chromium (100x coverage), and Hi-C sequencing data (63x coverage for reads containing Hi-C contacts). High-molecular weight DNA for the Nanopore, PacBio, and 10X Chromium libraries was isolated from 30 whole flash-frozen polyps using the Qiagen Gentra Puregene kit mouse tail protocol. The 10X Chromium libraries were sequenced using an Illumina HiSeq X Ten sequencer, the PacBio libraries were sequenced using a PacBio Sequel II sequencer, and the Nanopore libraries were sequenced using an Oxford Nanopore PromethION sequencer. The Hi-C library was also generated using 30 flash-frozen polyps that were then processed using the Arima-HiC Small Animal Tissue Kit and sequenced on an Illumina NovaSeq 6000 sequencer.

The Innsbruck female12 strain of H. oligactis is a clonally propagated line originating from a single polyp collected by Bert Hobmayer from the Lake Piburger See in Tyrol, Austria.

The H. oligactis assembly was generated using Oxford Nanopore data (17x coverage). High-molecular weight DNA was isolated from ~100 whole Innsbruck female12 strain H. oligactis polyps using the Circulomics Nanobind Tissue kit. Sequencing libraries were generated using an Oxford Nanopore Ligation Sequencing Kit and were sequenced using an Oxford Nanopore MinION sequencer.

Extensive descriptions of the assembly and annotation process for both genome assemblies can be found at github.com/cejuliano/brown_hydra_genomes.

Hydra AEP Genome Project Team

Department of Molecular and Cellular Biology
University of California, Davis

     Jack F. Cazet, Ph.D.
     Stefan Siebert, Ph.D.
     Hannah Morris Little
     Abby S. Primack
     Celina E. Juliano, Ph.D.


Center for Molecular Biosciences
University of Innsbruck

     Philip Bertemes
     Matthias Achrainer
     Peter Ladurner, Ph.D.
     Bert Hobmayer, Ph.D.


Computational and Statistical Genomics Branch
Division of Intramural Research
National Human Genome Research Institute
National Institutes of Health

     Travis Moreland, M.S.
     Anh-Dao Nguyen, M.S.
     Mark T. Fredriksen
     Tyra G. Wolfsberg, Ph.D.
     Sumeeta Singh, M.S.
     Suiyuan Zhang, M.S.
     Andreas D. Baxevanis, Ph.D.


Department of Molecular Evolution and Development
University of Vienna

     Oleg Simakov, Ph.D.


Whitney Laboratory for Marine Bioscience
University of Florida

     Christine Schnitzler, Ph.D.