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The Hydra genome

The genome of the freshwater cnidarian Hydra, a model organism used in evo-devo research, was recently deciphered by an international group of researchers including Prof. Thomas Holstein’s group from the University of Heidelberg. The sequencing of the Hydra genome sheds light on the early evolutionary lines and the development of the complexity of multicellular animals.

Hydra with young polyps that become detached from the parent when fully grown © biotechnologie.de

"In just twenty years, the quantity of DNA sequences in our databases has grown 40,000-fold, with the vast majority being added in the last decade. To put that number in perspective, in 1982 our total knowledge of DNA sequences from all living species amounted to less than one million characters. If printed onto pages like the ones you are reading, that amount of text would fit easily into one volume about the size of this book. If all of the DNA text that we now have was printed into volumes and stacked, they would be twice as high as the 110-storey Sears Tower in Chicago. This library of life is growing by more than 30 storeys per year" (quoted from: Sean B. Carroll's preface in "The Making of the Fittest": https://www.gesundheitsindustrie-bw.deseanbcarroll.com/books/The_Making_of_the_Fittest/excerpt/).

The technological progress of molecular biology, in particular of DNA sequencing, has uncovered information about evolutionary events that previous generations of researchers would not even have dared to dream about. Our knowledge about the origin and relationship of organisms has been radically changed thanks to our explosively increasing knowledge of the evolutionary traits contained in DNA. We now know that it is not just animals that are closely related to humans and plants, researchers' favourite experimental models are now many and varied (from E. coli to mice), and scientific curiosity and thirst for knowledge about living organisms is growing exponentially.

Consortium consisting of 20 groups of researchers

Prof. Dr. Thomas W. Holstein, Director, Institute of Zoology, University of Heidelberg © University of Heidelberg

The genome sequence of the freshwater cnidarian Hydra magnipapillata, one of the simplest multicellular animals (Metazoa) was recently published. Despite its alleged primitiveness, Hydra has a large, complex genome of 1.0 to 1.5 billion basepairs and around 20,000 protein-encoding genes. This corresponds approximately to the number of Caenorhabditis elegans genes. The number of genes in Hydra is considerably higher than that of Drosophila and slightly lower than the number of genes in highly developed organisms such as humans, mouse, pufferfish (Tetraodon nigroviridis) and thale cress (Arabidopsis thaliana). As is standard practice with such projects, the Hydra genome was sequenced by a large international consortium. The original publication lists 74 authors from twenty teams of researchers from the USA, Germany, Japan and Austria. The project was financed by the German Research Foundation, the American National Science Foundation, the National Human Genome Research Institute, the Japanese National Institute of Genetics and the Austrian Fund for the Promotion of Scientific Research. Major parts of the research were carried out by the team led by Prof. Dr. Thomas Holstein from the Department of Molecular Evolution and Genomics at the Institute of Zoology at the University of Heidelberg.

Hydra as evo-devo model

Abraham Trembley, philosopher, diplomat, born in Geneva in 1710, died in 1784. © Russian Academy of Sciences

Holstein has long used Hydra as a key model for investigating the evolution of developmental processes of organisms. This new area of research, often referred to as "evo-devo", i.e. evolutionary developmental biology research, has provided us with fundamental insights into the development of complex biological structures and metabolic pathways. People interested in the history of the natural sciences will not find the choice of Hydra as model organism unusual. Hydra was first described by Antoni van Leeuwenhoek in 1702. Since then the use of the organism, which is difficult to discern in water when attached to plants and catching water fleas and other small organisms with its 6 to 8 tentacles, in biological research has led to critical discoveries in experimental biology. Between 1740 and 1745, the Swiss natural scientist Abraham Trembley was the first to describe the asexual reproduction of Hydra by way of budding. Trembley also carried out admirable experiments designed to study the regeneration of the animal from individual tissue segments; he observed phototaxis in an eyeless organism and carried out the first successful transplantation of animal tissue. Nowadays, Hydra is an important model for stem cell biology and regeneration, embryonic development (a "kind of permanent embryo" according to the American researcher R. J. Davenport) and the differentiation of body axes.

The evolution of true tissue animals

Hydra, along with around 2,700 to 3,000 other, mainly marine species, belongs to the taxonomic class of Hydrozoa (phylum: Cnidaria, to which the classes Scyphozoa (the majority of jellyfish) and Antozoa (sea anemones and the majority of corals) also belong. Cnidaria have a radial symmetric form and they are regarded (potentially together with the genus Ctenophora) as phylogenetic sister groups of bilateral symmetric Bilataria, which comprise all other true multicellular animals, including humans. Based on DNA analyses, the common ancestor from which Cnidaria and Bilataria developed is assumed to have lived around 700 million years ago. But these are only rough estimates; fossils have not provided any information to substantiate this. The latest finds, which are classified (though controversially) as Cnidaria, were discovered in the Ediacaran fauna of the Upper Precambrian (about 600 to 545 million years ago).

The sea anemone Nematostella vectensis © Nature 2005

It is assumed that the first animals with true tissue (so-called Eumetazoa) had a bauplan (body plan) that is very similar to modern Cnidaria such as Hydra. It is further assumed that the multicellular composition of the animals arose as a result of the loss of rigid cell walls (plants and fungi). This enabled the animals to form cell contacts, enabling cell adhesion and communication between cells. Loose cell layers were transformed into structured epithelia. Early Eumetazoa are assumed to be diploblastic, just like modern Cnidaria. This means that they only consist of two epithelial layers, an outer and an inner one (ectoderm and endoderm), which surround the inward-facing intestine. The two epithelial layers surround a central cavity into which extracellular support substances are excreted. Cells, which however are unable to form tissue, are able to migrate into this gelatinous matrix, which is very extensive in many Cnidaria, in particular in jellyfish. Triploblastic Bilataria have a third epithelial cell layer (mesoderm) between these epithelia, which in the course of evolution led to the differentiation of inner organs.

The Hydra genome is of particular interest because it provides information about the genetic repertoire of higher animals. It is a matter of luck that sequences of the sea anemone Nematostella vectensis are available and can be compared with the Hydra sequences. Holstein and his team showed in 2005 in Nematostella vectensis that the Wnt gene family (which encodes secretory signalling proteins that control cell differentiation and embryogenesis and also plays a role in tumour pathogenesis) is as complex as that of vertebrate animals, including humans. These findings came as a total surprise since well-known animals such as Drosophila and Caenorhabditis have a much simpler Wnt pattern and it was assumed that the more primitive cnidarian also had a much simpler Wnt pattern.

Plea against primitiveness

It must not be concluded from these findings that Hydra and similar organisms are more closely related to humans in evolutionary terms than Drosophila and Caenorhabditis. The last common ancestor of Cnidaria and human beings is also the last common ancestor of all Bilataria. However, the evolutionary line that has led to the Protostomia (including Drosophila and C. elegans) has reduced the complexity of the Wnt gene pattern. Cnidaria have had the same time of evolution as humans, and they cannot be called primitive. Although they have conserved the simple bauplan of early Precambrian metazoans, they have nevertheless undergone considerable differentiations in other areas. They possess harpoon-like cnidae which led to the name Cnidaria. Cnidaria, and Cnidaria alone, probably has the most complicated intracellular biochemical apparatus in the world of organisms. Some species such as the tropical box jellyfish or Cynea capillata, which is known to Sherlock Holmes fans, produce the most effective and dangerous animal poison. Luckily, the model animals Hydra and Nematostella are harmless to humans. According to the famous biologist Edward O. Wilson, some Cnidaria (i.e. the siphonophores) have the same highly differentiated “state form” as social insects and humans, while simple coral polyps have most likely contributed more than any other organism to the development of reefs and hence to the earth’s geography.

The analysis of the Hydra genome shows that these simple multicellular organisms have developed many of the molecular switches that are required for the differentiation of higher organisms. The comparison of the Hydra genome with the genomes of other animals casts light on the evolution of epithelia, nervous and contractile tissue, the development of neuromuscular cell-cell contacts (junctions), the cell communication with receptors and signalling proteins and transcription factors which govern the embryonic and individual development of organisms.


Chapman JA, Kirkness EF, Simakov O et al.: The dynamic genome of Hydra. Nature 464: 592-596 (2010).

Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, Schmidt HA, Technau U, von Haeseler A, Hobmayer B, Martindale MQ, Holstein TW: Complexity of the Wnt gene family in a sea anemone. Nature 433: 156-160 (2005)

Further information:
Dr. Ernst-Dieter Jarasch
BioRegion Rhein-Neckar-Dreieck e.V.
E-mail: jarasch(at)bioregion-rnd.de
Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/the-hydra-genome