ArticleGenome biology and evolution2012
LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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Who cites it
106 citing papers in PubMed, 202 citations in OpenAlex.
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- Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae).G3 (Bethesda, Md.) · 2026Article
- Skin Colour in Salamanders Is Modulated by Both Epitranscriptomic Methylation and Gene Expression.Molecular ecology · 2026Article
- The dynamics of transposable element content in the genome of the human pathogen Histoplasma.Fungal genetics and biology : FG & B · 2026Article
- Unlocking Demography: Developing an eDNA-Based Toolkit to Measure Sex Ratios From Populations.Molecular ecology resources · 2026Article
- Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history.BMC genomics · 2025Article
- ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data.Genome biology · 2025Article
- The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians.iScience · 2025Article
- Linkage Mapping vs. Association: A Comparison of Two RADseq-Based Approaches to Identify Markers for Homomorphic Sex Chromosomes in Large Genomes.Molecular ecology resources · 2025Article
- The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus).G3 (Bethesda, Md.) · 2025Article
- Recursive splicing-a mechanism of intron removal with an unexplored role in the largest genomes.Journal of molecular evolution · 2025Review
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- Genome size evolution and phenotypic correlates in the poison frog family Dendrobatidae.Evolution; international journal of organic evolution · 2025Article
- Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus).Genome biology and evolution · 2025Article
- Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.Cell genomics · 2025Article
- Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.Molecular ecology resources · 2025Article
- The evolutionary dynamics of genome sizes and repetitive elements in Ensifera (Insecta: Orthoptera).BMC genomics · 2024Article
- Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.Molecular biology and evolution · 2024Article
- The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.BMC genomics · 2024Review
- The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.bioRxiv : the preprint server for biology · 2024Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.