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Cited by 100Chromosomal and Genetic VariationsGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

The contribution of transposable elements to size variations between four teleost genomes

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Gao, Bo, Shen, Dan, Xue, Songlei, Chen, Cai, Cui, Hengmi, Song, Chengyi·2016·Mobile DNA
DOI 10.1186/s13100-016-0059-7PMC PMC4746887
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Abstract

BACKGROUND: Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained. RESULTS: In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome. CONCLUSION: Overall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome 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 [58]

    The Results section (‘Dramatically different expansion of TEs across the four teleost genomes’; page unavailable) reports lower abundances of both DNA transposons and LTR retrotransposons in the smaller genomes. But the Abstract Results and Discussion (‘TE proliferation and genomic expansion in teleosts’; pages unavailable) identify DNA transposons—not LTR elements and DNA transposons jointly—as the main contributor to the differences. The paper compares TE accumulation across four teleosts; it does not establish depletion caused by reductions in both classes. (LLM, conf=0.86)

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Cited by

Sorted by citations

Authors
Gao, B., Shen, D., Xue, S., Chen, C., Cui, H., & Song, C.
Affiliations
Yangzhou University (CN)
Corresponding author
  • Cui, Hengmi
  • Song, Chengyi
ORCID
Venue
Mobile DNA
Publisher
Springer Science and Business Media LLC
Published
2016-02-09
Volume
7
Issue
1
Pages
4-4
ISSN
1759-8753 (ISSN-L)
DOI
10.1186/s13100-016-0059-7
PMC
PMC4746887
OpenAlex
W2263391408
Cited by
100
References
3
Citations by year
2026: 8 · 2025: 12 · 2024: 14 · 2023: 10 · 2022: 11 · 2021: 13 · 2020: 15 · 2019: 6 · 2018: 4 · 2017: 4 · 2016: 2 · 2012: 1
FWCI
5.46
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Mobile DNA (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Natural Science Foundation of China (31200920)
  • National Major Transgenic Project of China (2014ZX08006005-008)
  • Priority Academic Program Development of Jiangsu Higher Education Institutions
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, genome size variation, teleosts, DNA transposons, retrotransposons, hAT transposons, Tc1/mariner transposons, transposon activity, zebrafish, medaka, stickleback, Tetraodon, genome evolution

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