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Cited by 129Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic StudiesMarine Sponges and Natural Products

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

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Kenny, Nathan J., Francis, Warren R., Rivera-Vicéns, Ramón E., Juravel, Ksenia, de Mendoza, Alex, Díez-Vives, Cristina, Lister, Ryan, Bezares-Calderón, Luis A. +9 more·2020·Nature Communications
DOI 10.1038/s41467-020-17397-wPMC PMC7385117

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Abstract

The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.

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  • By 2020 and 2021, technological and algorithmic advances culminated in publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including jellyfish Rhopilema esculentum, sponge Ephydatia muelleri, and ctenophore Hormiphora californiensis.

    “By 2020 and 2021, these technological and algorithmic advances culminated in the publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including the jellyfish Rhopilema esculentum (92), the sponge Ephydatia muelleri (93), and the ctenophore Hormiphora californiensis (57).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [93]

    The Introduction identifies this paper as presenting a chromosome-level assembly of the sponge Ephydatia muelleri. But the Results and discussion section reports that only 83.7% of the genome lies in the largest 24 scaffolds, with the remainder in smaller scaffolds; it therefore does not support calling the assembly complete. The citation is attached to the sponge, not the other two animals. (LLM, conf=0.86)

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Authors
Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderón, L. A., Grombacher, L., Roller, M., Barlow, L. D., Camilli, S., Ryan, J. F., Wörheide, G., Hill, A. L., Riesgo, A., & Leys, S. P.
Affiliations
  • Oxford Brookes University (GB)
  • University of Southern Denmark (DK)
  • Ludwig-Maximilians-Universität München (DE)
  • The University of Western Australia (AU)
  • University of Exeter (GB)
  • University of Alberta (CA)
  • European Bioinformatics Institute (GB)
  • Bates College (US)
  • University of Florida (US)
  • Bayerische Staatssammlung für Paläontologie und Geologie (DE)
  • Natural History Museum (GB)
Corresponding author
  • Kenny, Nathan J.
  • Leys, Sally P.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2020-07-27
Volume
11
Issue
1
Pages
3676-3676
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-020-17397-w
PMC
PMC7385117
OpenAlex
W3044935310
Cited by
129
References
12
Citations by year
2026: 16 · 2025: 21 · 2024: 29 · 2023: 22 · 2022: 16 · 2021: 22 · 2020: 3
FWCI
8.74
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by)
  • UWA Profiles and Research Repository (UWA) (submittedVersion, cc-by)
  • Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
  • University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion, cc-by)
Funders
Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (RGPIN-2016-05446)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Marine Sponges and Natural Products
Keywords
Ephydatia muelleri, freshwater sponges, sponges, genome assembly, early animal evolution, synteny, gene duplication, thermal adaptation, DNA methylation, symbiotic bacteria
MeSH terms
RNA-Seq, Adaptation, Physiological, Animals, Chromosome Mapping, Chromosomes, Fresh Water, Phylogeny, Porifera, Sequence Analysis, DNA, Gene Expression Regulation, Developmental, Evolution, Molecular, Synteny, Epigenesis, Genetic, Molecular Sequence Annotation

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