The Amphimedon queenslandica genome and the evolution of animal complexity
Open accessAbstract
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.
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Scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning divergence between cnidarians, chordates, sponges, and placozoans.
“scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning the divergence between cnidarians, chordates, sponges, and placozoans”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [37]
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 [37]
Sequencing of the Amphimedon queenslandica genome and multiple transcriptomes from all major sponge lineages revealed a remarkable number of genes present in sponges that are associated with neural cell types in bilaterians and cnidarians.
“Sequencing of the demosponge genome Amphimedon queenslandica [32] and multiple transcriptomes from all major sponge lineages [33] have revealed a remarkable number of genes present in sponges that are associated with neural cell types in bilaterians and cnidarians.”
From Where is my mind? How sponges and placozoans may have lost neural cell types (2015) · cites this paper as [32]
Sponges have genes associated with neurons, behaviours indicating sensing of external stimuli, and secretory cells involved in sensory behaviour that express neural genes.
“Sponges are said to lack true neural cell types [31], yet these animals have genes associated with neurons, behaviours indicating sensing of external stimuli, and secretory cells involved in sensory behaviour that express neural genes.”
From Where is my mind? How sponges and placozoans may have lost neural cell types (2015) · cites this paper as [32]
Most structural components of the post-synaptic density are present in the sponge Amphimedon, and some have homologs in choanoflagellates and other unicellular holozoans.
“most of the structural components of the post-synaptic density (PSD) are present in the sponge Amphimedon [22,28], and some have clear homologs in choanoflagellates and other unicellular holozoans [29,30]”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [22]
Genomic and transcriptomic databases are becoming available for several sponge species and for the placozoan Trichoplax adhaerens.
“an extensive set of genomic and transcriptomic databases is becoming available for several sponge species -Amphimedon queenslandica, Oscarella carmela and Sycon ciliatum, as well as for a placozoan Trichoplax adhaerens [22–25]”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [22]
It is more probable that the first neurons with fast electrical signal propagation to evolve were controlling animal locomotion.
“Although neurosecretory systems have deep ancestry in metazoan evolution [1,2], it is more probable that the first neurons with fast electrical signal propagation to evolve were controlling animal locomotion.”
From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [1]
Even if a local release of transmitters is possible in sponges, the effects of such signal transmission can only be local, since sponges have no gap junctions and no axons.
“Even if a local release of transmitters is possible in sponges, the effects of such signal transmission can only be local, since sponges have no gap junctions and no axons [1].”
From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [1]
These GPCRs originated by lineage-specific expansion, and many are single-exon genes forming clusters in the genome, reminiscent of lineage-specific putative chemosensory GPCRs in other animal groups.
“These GPCRs originated by lineage-specific expansion, and many are single-exon genes forming clusters in the genome [1], reminiscent of lineage-specific putative chemosensory GPCRs in other animal groups [43].”
From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [1]
The sponge genome contains genes coding for neuropeptide processing enzymes and synaptic vesicle release proteins, but no neuropeptides have been identified.
“The sponge genome contains genes coding for neuropeptide processing enzymes and synaptic vesicle release proteins, however no neuropeptides have been identified [1].”
From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [1]
The presence of approximately 130 rhodopsin-family G-protein coupled receptors (GPCRs) in the sponge genome suggests the use of chemosensation.
“The presence of approximately 130 rhodopsin-family G-protein coupled receptors (GPCRs) in the sponge genome also suggests the use of chemosensation [1].”
From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [1]
The developmental gene toolkit of sponges is surprisingly similar to the eumetazoan toolkit, although information on its expression remains limited.
“Importantly, the developmental gene toolkit of sponges is surprisingly similar to the eumetazoan toolkit, although information on its expression remains limited 4,7 .”
From Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans (2014) · cites this paper as [7]
One of the three Amphimedon Wnt ligands is specifically expressed in the posterior pole of embryos and larvae, and one of the eight Amphimedon Tgfb ligands is expressed in the outer embryonic layer and then restricted to the posterior pole.
“One of the three Amphimedon Wnt ligands is specifically expressed in the posterior pole of the embryos and larvae, and one of the eight Amphimedon Tgfb ligands is expressed in the outer embryonic layer, and then restricted to the posterior pole 7,48 .”
From Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans (2014) · cites this paper as [7]
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- Authors
- Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., Richards, G. S., Conaco, C., Dacre, M., Hellsten, U., Larroux, C., Putnam, N. H., Stanke, M., Adamska, M., Darling, A., Degnan, S. M., Oakley, T. H., Plachetzki, D. C., Zhai, Y., Adamski, M., Calcino, A., Cummins, S. F., Goodstein, D. M., Harris, C., Jackson, D. J., Leys, S. P., Shu, S., Woodcroft, B. J., Vervoort, M., Kosik, K. S., Manning, G., Degnan, B. M., & Rokhsar, D. S.
- Affiliations
- University of California, Berkeley (US)
- University of Zurich (CH)
- Joint Genome Institute (US)
- The University of Queensland (AU)
- University of California, Santa Barbara (US)
- Salk Institute for Biological Studies (US)
- Rice University (US)
- University of Göttingen (DE)
- University of California, Davis (US)
- University of Alberta (CA)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Srivastava, Mansi
- ORCID
- Venue
- Nature
- Published
- 2010-08
- Volume
- 466
- Issue
- 7307
- Pages
- 720-726
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3130542
- OpenAlex
- W340499956
- Semantic Scholar
- c40c8376e81b11bf8f3e7d04f22db8b3568f06e7
- Cited by
- 1,049
- References
- 60
- Citations by year
- 2026: 22 · 2025: 36 · 2024: 45 · 2023: 56 · 2022: 59 · 2021: 47 · 2020: 51 · 2019: 70 · 2018: 71 · 2017: 60 · 2016: 63 · 2015: 99 · 2014: 85 · 2013: 79 · 2012: 101
- FWCI
- 64.30
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion)
- PubMed Central (acceptedVersion)
- QUT ePrints (Queensland University of Technology) (submittedVersion, cc-by-nc-sa)
- ResearchOnline at James Cook University (James Cook University) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Lawrence Berkeley National Laboratory
- Funders
- National Science Foundation (DEAC02-05CH11231)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Gordon and Betty Moore Foundation
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- Deutsche Forschungsgemeinschaft (DE-AC02-05CH11231)
- Agence Nationale de la Recherche (DE-AC02-05CH11231)
- Centre National de la Recherche Scientifique (DE-AC02-05CH11231)
- National Institutes of Health (DE-AC02–05CH11231)
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
- Australian Research Council
- National Human Genome Research Institute (DE-AC02-05CH11231, R01HG004164)
- 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
- Amphimedon queenslandica, sponge genome, demosponges, origin of animals, transcription factors, signaling pathways, cell cycle regulation, cell adhesion, innate immunity, allorecognition, germ cell specification, multicellularity, cancer, comparative genomics
- MeSH terms
- Animals, Cell Adhesion, Cell Cycle, Genes, Humans, Immunity, Innate, Models, Biological, Neurons, Phosphotransferases, Phylogeny, Porifera, Signal Transduction, Genome, Cell Polarity, Apoptosis, Sequence Analysis, DNA, Evolution, Molecular, Genomics, Cell Proliferation
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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