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Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history

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Rubio, Andrew O., Neddermeyer, John H., James, Aakash, Janz, Nicholas, Rader, Jonathan A., Tollis, Marc, Stuckert, Adam M. M.·2025·BMC Genomics
DOI 10.1186/s12864-025-12414-yPMC PMC12822217

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Abstract

Background: Transposable elements (TEs), often referred to as ‘selfish genetic elements’, hijack their host’s genetic machinery to replicate themselves within the host genome, and are primary contributors to genome size in vertebrates. In particular, frogs and toads (Order: Anura) are well known for not only having large genomes, but for having genomes with drastic variation in size (e.g., Scaphiopus couchii : 0.48 Gbp, Rana muscosa 10 Gbp). This discrepancy in size is due in part to relative differences in the proliferation and success of TEs across anuran genomes. In this study, we ask: do specific TE families drive genome size variation and are these patterns phylogenetically-constrained? To answer this, we use 61 publicly available anuran reference genome assemblies, comprising 22 anuran families, to investigate the effects of TEs on the evolution of anuran genome size. In addition, we used repeat landscapes to analyze TE activity in the context of anuran evolutionary history, in order to understand how lineage-specific TE activity affects genome size variation in anurans. Finally, we examined how life history traits that have been predicted to be constrained by genome size, larval period and clutch size, are associated with TEs. Results: Our results suggest that copy number of elements and total content of several TEs families (L1/CIN4, Ty1/Copia, Ty3/DIRS1, hobo-Activator) are associated with increased genome size across anurans. We further found that the copy numbers of recently active Ty3 retrotransposons are correlated with increased genome size, suggesting that expansions of this family of TE have had a distinct effect on the size of the anuran genome across evolutionary time. Finally, we found interactions between several TE families (hobo-Activator, PiggyBac, L2/CR1/Rex, and SINEs) and larval period, indicating that developmental time may be a major constraint on genome size and species with additional constraints may more effectively purge TEs. Conclusion: Our findings underscore the pivotal roles of both the activity of specific TE families (L1/CIN4, Ty1/Copia, Ty3/DIRS1, hobo-Activator) and developmental constraints in amphibian genome size evolution.

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  • The primary causes of TE depletion were reduction of LTR elements and DNA transposons, which are highly active element classes capable of rapid genome expansion.

    “The primary causes of TE depletion were reduction of LTR elements and DNA transposons which are highly active element classes capable of rapid genome expansion (57–62).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [60]

    The Discussion section on transposable-element families says LTR elements can proliferate in bursts and rapidly increase genome size; it also links a DNA transposon family to genome expansion. It does not identify reductions in LTR elements and DNA transposons as the primary causes of TE depletion. The indexed passages provide no page numbers. (LLM, conf=0.84)

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Authors
Rubio, A. O., Neddermeyer, J. H., James, A., Janz, N., Rader, J. A., Tollis, M., & Stuckert, A. M. M.
Affiliations
  • University of Houston (US)
  • Northern Arizona University (US)
  • Texas A&M International University (US)
Corresponding author
  • Rubio, Andrew O.
  • Tollis, Marc
  • Stuckert, Adam M. M.
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2025-12-18
Volume
27
Issue
1
Pages
74-74
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/s12864-025-12414-y
PMC
PMC12822217
OpenAlex
W4417448679
Cited by
2
References
1
Citations by year
2026: 2
FWCI
0.93
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
Funders
National Science Foundation (NSF DEB 2323124, NSF IOS-2319712)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
genome size evolution, transposable elements, retrotransposons, Anura, Ty1-copia, piggyBac, SINEs, larval period, clutch size, life history, transposable element copy number, phylogenetic constraints
MeSH terms
Animals, Anura, Phylogeny, Retroelements, Evolution, Molecular, Genome Size

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