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Hydra Genome Sequenced by J. Craig Venter Institute and Multi-National Research Team

Research marks a major step toward understanding the molecular "toolbox" of the animal kingdom's earliest common ancestors

ROCKVILLE, MD — March 14, 2010 — Researchers from the J. Craig Venter Institute, along with more than 70 other researchers from around the world, have sequenced and analyzed the genome of Hydra magnipapillata, a fresh water member of the cnidaria--  stinging animals that include jellyfish, sea anemones and corals.

The research, published in the March 14 edition of Nature, was co-led by Ewen F. Kirkness, JCVI, Jarrod A. Chapman, Department of Energy Joint Genome Institute, and Oleg Simakov, University of California, Berkeley. This is the second sequenced cnidarian genome, following that of a sea anemone, Nematostella vectensis, in 2007. The ancestors of these two species diverged more than 500 million years ago, and comparison of their genomes has revealed common features of the earliest animals that gave rise to the diversity of animals on Earth today. Unexpectedly, the sequencing also revealed a novel bacterium that lives in close association with the Hydra.

Hydra have been studied for more than 300 years, and have been found to display several unusual properties such as, asexual reproduction and the ability to regenerate. However, the genome sequence is enabling a much deeper understanding of the organism's evolutionary history and the genes that are responsible for some of those unique characteristics.

The Hydra genome was sequenced at the JCVI, and assembled independently by the JCVI and JGI.  The genome is approximately one billion base pairs in size and contains approximately 20,000 protein coding genes. The team found clear evidence for conserved genome structure between the Hydra and other animals, like humans. This contrasts with organisms like the fruit fly (Drosophila) and the roundworm (C. elegan), where gene order has been shuffled extensively.

The Hydra genome is twice as large as the sea anemone genome, which is mainly due to transposons (parasitic segments of DNA that can replicate and move around in a genome or between genomes) from more than 500 different families. By looking at the sequence of these transposons the team was able to discern three distinct periods in Hydra's ancestry when transposons were particularly active at invading Hydra's genome. These may have resulted in the formation of new Hydra species.

Most of the genes in a genome are acquired from parents, though there are also rarer instances of gene acquisition from other species via bacterial or viral transmission. The existence of such horizontal gene transfer in Hydra was confirmed and expanded upon by the teams' discovery of 71 Hydra genes that are more closely related to genes from bacteria than those from animals. The team also found 90 transposable elements that were most likely horizontally transferred to the Hydra in the recent past.

The Hydra is missing several genes found in the sea anemone genome that are of potential developmental significance. These correspond to larvae development in the sea anemone, which the Hydra no longer goes through. The Hydra is also missing key genes for fluorescent proteins and circadian rhythms.

It is well established that Hydra has pluripotent stem cells that produce germ, nerve, nematocytes and secretory cells. However, the Hydra does not have three of the five genes that mammals use to induce pluripotency in somatic cells. Thus, the team surmises that the evolutionary origin for these stem cells is different in Hydra than in mammals. Despite the absence of most of the key genes for stem cell pluripotency, the Hydra has a system that is very similar to mammals.

Early in the evolution of animals, a few genome designs were particularly successful, and their descendants evolved into the rich diversity of animal species on Earth today. According to Dr. Kirkness, "As we sequence more genomes that have descended from these early branches, we begin to resolve the genetic toolbox that was necessary for animals to evolve successfully on Earth. The Hydra genome sequence provides a critical piece of this puzzle."

Funding for this research was provided by the National Institutes of Health's National Human Genome Research Institute.

About the J. Craig Venter Institute

The JCVI is a not-for-profit research institute in Rockville, MD and San Diego, CA dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 400 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c)(3) organization. For additional information, please visit http://www.weizhongli-lab.org.

Media Contact

Heather Kowalski, hkowalski(AT)jcvi.org; 301-943-8879