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International Team Sequences Hydra Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper appearing in the online version of Nature yesterday, an international research team led by investigators at US Department of Energy's Joint Genome Institute, the J. Craig Venter Institute, the University of Heidelberg, and the University of California reported that they have sequenced the genome of the Hydra magnipapillata, a freshwater cnidarian.

The researchers used a whole-genome shotgun approach to generate draft genome sequence for the Hydra. In the process, they also sequenced the genome of a bacterial species in the Curvibacter genus that's associated with the animal.

Based on their results so far, those involved with the sequencing project say the H. magnipapillata genome shows evidence of horizontal gene transfer and extensive transposable element expansion. And, they say, comparing the Hydra genome with the genomes of other animals is providing valuable clues about animal evolution and development.

"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," co-lead author Ewen Kirkness, a genomic medicine researcher at JCVI, said in a statement. "The Hydra genome sequence provides a critical piece of this puzzle."

In 2007, researchers from JGI, UC Berkeley and elsewhere reported on the first cnidarian genome — that of the starlet sea anemone, Nematostella vectensis. For the current paper, researchers focused on Hydra, an animal with a genome roughly twice the size of the sea anemone genome.

Because the Hydra is capable of both asexual reproduction by budding and tissue regeneration, it is a useful model for studying everything from body plan patterning to stem cell function and regeneration, the researchers explained.

Collaborators at JCVI used whole-genome shotgun sequencing to sequence the genome of the H. magnipapillata strain 105. They then assembled two draft genome assemblies — a one billion base assembly and a 1.5 billion base assembly. Both assemblies have reportedly been deposited into GenBank.

In addition to the Hydra sequence, the researchers also generated sequence representing eight bacterial scaffolds that seem to belong to a new Curvibacter species that's stably associated with the Hydra.

During their subsequent analyses of the Hydra genome assembly showing minimal sequence redundancy, the researchers identified about 20,000 protein-coding genes, including several genes that appear to have originated from horizontal gene transfer.

The team also identified transposable elements from more than 500 families, which appear to make up some 57 percent of Hydra genome sequence and seem to explain the size difference between the Hydra and sea anemone genomes.

These transposable elements seem to have undergone at least three bursts of expansion in the Hydra genome, the researchers noted. And, they found, at least 90 of the transposable elements identified appear to have arisen through horizontal gene transfer.

In their subsequent analyses, the team not only compared the Hydra genome with that of the sea anemone and other animals, they also examined splicing patterns and non-coding sequence repertoires in Hydra as well as signaling pathways, developmental genes, and stem cell genetics.

For example, the researchers found that H. magnipapillata lacks three of the five genes that are known to coax mammalian somatic cells into pluripotent state. That suggests stem cells may have evolved differently in Hydra than in mammals.

"Having the Hydra genome sequenced also enhances our ability to use it to learn more about the basic biology of stem cells, which are showing great promise for new treatments for a host of injuries and diseases," senior author Robert Steele, a researcher at the University of California at Irvine and interim chair of the institute's biological chemistry department, said in a statement.

While the researchers say the current genome assembly is too fragmented for chromosomal analyses, they found that nearly half of the Hydra scaffolds contained genes found in other animal groups, suggesting the animal shares synteny with other metazoan animals.

"The sequencing of the Hydra genome has revealed unexpected relationships between the genetic makeup of the animal and its biology," the researchers wrote. "The availability of the Hydra genome sequence and methods to manipulate it provide an opportunity to understand how this remarkable animal evolved."