ArticleJournal of molecular evolution2015
Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.
Article in Journal of molecular evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
- Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features.Nature communications · 2026Article
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- DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions.Communications biology · 2025Article
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- Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.Molecular ecology resources · 2025Article
- Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.Molecular biology and evolution · 2024Article
- Transposable element and host silencing activity in gigantic genomes.Frontiers in cell and developmental biology · 2023Article
- The salamander blastema within the broader context of metazoan regeneration.Frontiers in cell and developmental biology · 2023Review
- Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development.Integrative organismal biology (Oxford, England) · 2023Article
- Transposable Element Diversity Remains High in Gigantic Genomes.Journal of molecular evolution · 2022Article
- Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds.Science advances · 2022Article
- Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression.Genome research · 2022Article
- Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux.Genome biology and evolution · 2022Article
- The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes.Genes · 2021Review
- A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog,Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
- A Field Guide to Eukaryotic Transposable Elements.Annual review of genetics · 2020Review
- Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.Molecular biology and evolution · 2018Article
- Coevolution between transposable elements and recombination.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes.Genome biology and evolution · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., <30 bp) deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.
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