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Cited by 28Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesGenome Rearrangement Algorithms

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Teleost genomic repeat landscapes in light of diversification rates and ecology

Open access
Reinar, William B., Tørresen, Ole K., Nederbragt, Alexander J., Matschiner, Michael, Jentoft, Sissel, Jakobsen, Kjetill S.·2023·Mobile DNA
DOI 10.1186/s13100-023-00302-9PMC PMC10546739
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Abstract

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

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  • Repeat element accumulation is a primary driver of genome size variation across Cypriniformes.

    “indicating that repeat element accumulation is a primary driver of genome size variation across the order (26–28)”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [27]

    The Results section reports that repeat counts correlate with genome assembly size across sampled teleosts. The Discussion says TE abundance alone explains 28% of genome-size variation, not that repeat accumulation is the primary driver. The paper does not establish that conclusion specifically for Cypriniformes. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

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Metadata

Authors
Reinar, W. B., Tørresen, O. K., Nederbragt, A. J., Matschiner, M., Jentoft, S., & Jakobsen, K. S.
Affiliations
University of Oslo (NO)
Corresponding author
  • Jentoft, Sissel
  • Jakobsen, Kjetill S.
ORCID
Venue
Mobile DNA
Publisher
Springer Science and Business Media LLC
Published
2023-10-03
Volume
14
Issue
1
Pages
14-14
ISSN
1759-8753 (ISSN-L)
DOI
10.1186/s13100-023-00302-9
PMC
PMC10546739
OpenAlex
W4387312183
Cited by
28
References
1
Citations by year
2026: 7 · 2025: 13 · 2024: 8
FWCI
4.06
Type
journal article
Language
en
Open access
Licence
Locations
  • Mobile DNA (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Duo Research Archive (University of Oslo) (submittedVersion, cc-by)
Funders
Norwegian Research Council (251076, 222378)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
repetitive DNA, transposable elements, teleosts, genome size, microsatellite markers, codfish, herring, mutational load, fecundity, genome annotation

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