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Cited by 386Chromosomal and Genetic VariationsGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

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Chalopin, Domitille, Naville, Magali, Plard, Floriane, Galiana, Delphine, Volff, Jean-Nicolas·2015·Genome Biology and Evolution
DOI 10.1093/gbe/evv005PMC PMC4350176
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Abstract

Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.

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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 [57]

    The Results (Lineage-Specific TE Activity during Vertebrate Evolution; page unavailable) describe bursts of LTR retroelements and DNA transposons, supporting their capacity to expand in genomes. The paper does not identify reductions in those two classes as the primary causes of TE depletion; the Discussion (Diversity of TE Contribution to Genome Size in Vertebrates; page unavailable) instead discusses variation in TE activity and elimination rates more generally. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Low-divergence copies of transposable elements represent more recent insertions, and highly diverged copies reflect older, inactive elements.

    “Low-divergence copies represent more recent insertions and highly diverged copies reflect older, inactive elements (53, 57, 61).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [57]

    The Results section (“Lineage-Specific TE Activity during Vertebrate Evolution”) says low-divergence copies indicate recent activity and highly divergent copies come from ancient transposition events. The Fig. 4 caption describes the latter as potentially ancient or degenerated, but does not establish that highly diverged copies are inactive. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

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Authors
Chalopin, D., Naville, M., Plard, F., Galiana, D., & Volff, J.-N.
Affiliations
Lyon 1 Université (FR)
Corresponding author
Volff, Jean-Nicolas
ORCID
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2015-01-09
Volume
7
Issue
2
Pages
567-580
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evv005
PMC
PMC4350176
OpenAlex
W2152222332
Cited by
386
References
4
Citations by year
2026: 25 · 2025: 32 · 2024: 36 · 2023: 26 · 2022: 43 · 2021: 45 · 2020: 40 · 2019: 39 · 2018: 32 · 2017: 29 · 2016: 25 · 2015: 13 · 2012: 1
FWCI
36.45
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Genome Biology and Evolution (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
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
transposable elements, transposable element evolution, DNA transposons, LINE retrotransposons, non-LTR retrotransposons, sarcopterygians, actinopterygian fishes, genome size, genome evolution, medaka, platyfish, zebrafish, pufferfish
MeSH terms
Animals, DNA Transposable Elements, Fishes, Phylogeny, Genetic Variation, Vertebrates, Genome, Retroelements, Evolution, Molecular, Long Interspersed Nucleotide Elements, Short Interspersed Nucleotide Elements, Genome Size

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