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Cited by 106Chromosomal and Genetic VariationsMarine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Topological structures and syntenic conservation in sea anemone genomes

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Zimmermann, Bob, Montenegro, Juan D., Robb, Sofia M. C., Fropf, Whitney J., Weilguny, Lukas, He, Shuonan, Chen, Shiyuan, Lovegrove-Walsh, Jessica +11 more·2023·Nature Communications
DOI 10.1038/s41467-023-44080-7PMC PMC10719294

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Abstract

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus . We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella . This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

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  • In non-bilaterian lineages such as cnidarians, available data suggest that topological domains are smaller, if they exist at all, and potentially less insulated.

    “By contrast, in non-bilaterian lineages such as cnidarians, available data suggest that topological domains are smaller, if they exist at all (134), and potentially less insulated (135).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [134]

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Cited by

Sorted by citations

Authors
Zimmermann, B., Montenegro, J. D., Robb, S. M. C., Fropf, W. J., Weilguny, L., He, S., Chen, S., Lovegrove-Walsh, J., Hill, E. M., Chen, C.-Y., Ragkousi, K., Praher, D., Fredman, D., Schultz, D., Moran, Y., Simakov, O., Genikhovich, G., Gibson, M. C., & Technau, U.
Affiliations
  • University of Vienna (AT)
  • Stowers Institute for Medical Research (US)
Corresponding author
  • Gibson, Matthew C.
  • Technau, Ulrich
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-12-13
Volume
14
Issue
1
Pages
8270-8270
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-44080-7
PMC
PMC10719294
OpenAlex
W4389676068
Cited by
106
References
16
Citations by year
2026: 26 · 2025: 23 · 2024: 22 · 2023: 18 · 2022: 9 · 2021: 8
FWCI
13.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Austrian Science Fund (P24858, P21108)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • 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
Keywords
Nematostella vectensis, chromosome-level genome assembly, Hox gene clusters, microsynteny, cis-regulatory sequences, topologically associating domains, 3D genome organization, long-range gene regulation, karyotype evolution
MeSH terms
Animals, Gene Expression Regulation, Phylogeny, Sea Anemones, Genome, Synteny

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