The dynamic genome of Hydra
Open accessAbstract
Hydra, first described by Anton van Leeuwenhoek in a letter to the Royal Society in 1702, has been studied by biologists for centuries and now is an important model for work on axial patterning, stem cell biology and regeneration. Its genome, over half of which is made up of mobile elements, has now been sequenced, as has the genome of a Curvibacter sp. bacterium stably associated with Hydra magnipapillata. Comparisons of the Hydra genome with those of other animals provide insights into the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, pluripotency genes and the neuromuscular junction, as well as the Spemann–Mangold organizer, the region in the early embryo that establishes the embryo's axis. The freshwater cnidarian Hydra is a significant model for studies of axial patterning, stem cell biology and regeneration. Its (A+T)-rich genome has now been sequenced. Comparison of this genome with those of other animals provides insights into the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, pluripotency genes and more. The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction.
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Genome sequences of sponges, placozoans, and cnidarians suggested that many genes thought to define vertebrates were present even in earlier ancestral animals.
“Genome sequences of some animal clades very distantly related to humans, including sponges (37), placozoans (flat animals) (38), and cnidarians (i.e., true jellyfish, corals) (39, 40), suggested that many genes thought to define vertebrates were, in fact, present even in earlier ancestral animals”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [39]
Much of the molecular architecture underlying neurogenesis and neuron functioning is conserved between bilaterians and cnidarians.
“The publication of several cnidarian genomes has shown that much of the molecular architecture underlying neurogenesis and neuron functioning is conserved between bilaterians and cnidarians [17,47–51].”
From Evolution of eumetazoan nervous systems: insights from cnidarians (2015) · cites this paper as [47]
Whole genome sequencing of Nematostella vectensis and Hydra magnipapillata offers the possibility to quickly gather an overview of the receptor complement in these species.
“The sequencing in recent years of the whole genome of different cnidarian species, most notably those of the anthozoan Nematostella vectensis and the hydrozoan Hydra magnipapillata (Figure 1) [50,51], has offered the exciting possibility to quickly gather an overview on the entire complement of receptors in these species.”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [51]
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- Authors
- Chapman, J. A., Kirkness, E. F., Simakov, O., Hampson, S. E., Mitros, T., Weinmaier, T., Rattei, T., Balasubramanian, P. G., Borman, J., Busam, D., Disbennett, K., Pfannkoch, C., Sumin, N., Sutton, G. G., Viswanathan, L. D., Walenz, B., Goodstein, D. M., Hellsten, U., Kawashima, T., Prochnik, S. E., Putnam, N. H., Shu, S., Blumberg, B., Dana, C. E., Gee, L., Kibler, D. F., Law, L., Lindgens, D., Martinez, D. E., Peng, J., Wigge, P. A., Bertulat, B., Guder, C., Nakamura, Y., Ozbek, S., Watanabe, H., Khalturin, K., Hemmrich, G., Franke, A., Augustin, R., Fraune, S., Hayakawa, E., Hayakawa, S., Hirose, M., Hwang, J. S., Ikeo, K., Nishimiya-Fujisawa, C., Ogura, A., Takahashi, T., Steinmetz, P. R. H., Zhang, X., Aufschnaiter, R., Eder, M.-K., Gorny, A.-K., Salvenmoser, W., Heimberg, A. M., Wheeler, B. M., Peterson, K. J., Böttger, A., Tischler, P., Wolf, A., Gojobori, T., Remington, K. A., Strausberg, R. L., Venter, J. C., Technau, U., Hobmayer, B., Bosch, T. C. G., Holstein, T. W., Fujisawa, T., Bode, H. R., David, C. N., Rokhsar, D. S., & Steele, R. E.
- Affiliations
- Joint Genome Institute (US)
- J. Craig Venter Institute (US)
- Heidelberg University (DE)
- University of California, Irvine (US)
- University of California, Berkeley (US)
- Technical University of Munich (DE)
- Salk Institute for Biological Studies (US)
- Christian-Albrechts-Universität zu Kiel (DE)
- National Institute of Genetics (JP)
- University of Vienna (AT)
- University of Kansas Medical Center (US)
- Universität Innsbruck (AT)
- Dartmouth College (US)
- North Carolina State University (US)
- Ludwig-Maximilians-Universität München (DE)
- Corresponding author
- Rokhsar, Daniel S.
- Steele, Robert E.
- ORCID
- Simakov, Oleg
- Mitros, Therese
- Weinmaier, Thomas
- Rattei, Thomas
- Walenz, Brian
- Goodstein, David M.
- Kawashima, Takeshi
- Putnam, Nicholas H.
- Blumberg, Bruce
- Dana, Catherine E.
- Wigge, Philip A.
- Guder, Corina
- Nakamura, Yukio
- Watanabe, Hiroshi
- Khalturin, Konstantin
- Franke, André
- Fraune, Sebastian
- Hayakawa, Eisuke
- Hirose, Mamiko
- Hwang, Jung Shan
- Ikeo, Kazuho
- Steinmetz, Patrick R. H.
- Zhang, Xiaoming
- Salvenmoser, Willi
- Peterson, Kevin J.
- Böttger, Angelika
- Wolf, Alexander
- Gojobori, Takashi
- Venter, J. Craig
- Technau, Ulrich
- Hobmayer, Bert
- Bosch, Thomas C. G.
- Holstein, Thomas W.
- David, Charles N.
- Rokhsar, Daniel S.
- Steele, Robert E.
- Venue
- Nature
- Published
- 2010-03
- Volume
- 464
- Issue
- 7288
- Pages
- 592-596
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4479502
- OpenAlex
- W2031493923
- Cited by
- 810
- References
- 26
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- FWCI
- 50.55
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Science Foundation (0120591, DEAC02-05CH11231, 0716960)
- U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
- Gordon and Betty Moore Foundation
- Alexander von Humboldt-Stiftung (DE-AC02-05CH11231)
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- Toyobo Biotechnology Foundation
- Deutsche Forschungsgemeinschaft (DE-AC02-05CH11231, SFB 488)
- Austrian Science Fund (P 20734, P 16685, DE‐AC02‐05CH11231)
- Norges Forskningsråd (DE-AC02-05CH11231)
- Exzellenzclusters Entzündungsforschung
- Office of Science (No. DE-AC02- 05-CH11231, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231, Contract No. DE-AC02-05CH11231)
- Japan Society for the Promotion of Science
- National Human Genome Research Institute (DE-AC02-05CH11231)
- National Center for Research Resources (R24RR015088)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Hydra magnipapillata, genome sequencing, transposable elements, horizontal gene transfer, trans-splicing, symbiotic bacteria, Nematostella vectensis, axial patterning, Spemann-Mangold organizer, pluripotency genes, neuromuscular junction, transcription factors, regeneration, stem cell biology
- MeSH terms
- Animals, DNA Transposable Elements, Hydra, Molecular Sequence Data, Neuromuscular Junction, Genome, Genome, Bacterial, Gene Transfer, Horizontal, Anthozoa, Comamonadaceae
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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