ArticleGenomics, proteomics & bioinformatics2021
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.
Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks.Genome biology · 2026Article
- A comparative transcriptomic analysis provides new insights into the ecological adaptations in Ichthyophis bannanicus.BMC genomics · 2025Article
- Genome size evolution and phenotypic correlates in the poison frog family Dendrobatidae.Evolution; international journal of organic evolution · 2025Article
- DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions.Communications biology · 2025Article
- Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus).Genome biology and evolution · 2025Article
- Article
- Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.Molecular ecology resources · 2025Article
- Multi-omics analysis reveals the evolution, function, and regulatory mechanisms of SPF pheromones in Anurans.Communications biology · 2024Article
- Transposable Element Diversity and Activity Patterns in Neotropical Salamanders.Molecular biology and evolution · 2024Article
- Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles.Molecular biology and evolution · 2024Article
- Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior.G3 (Bethesda, Md.) · 2023Article
- Comparative genomics reveals insights into anuran genome size evolution.BMC genomics · 2023Article
- Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.Molecular biology and evolution · 2023Article
- Insights into mammalian TE diversity through the curation of 248 genome assemblies.Science (New York, N.Y.) · 2023Article
- Transposable element and host silencing activity in gigantic genomes.Frontiers in cell and developmental biology · 2023Article
- Genome-Wide Survey and Development of the First Microsatellite Markers Database (International journal of molecular sciences · 2022Article
- Morphological and molecular evolution of hadal amphipod's eggs provides insights into embryogenesis under high hydrostatic pressure.Frontiers in cell and developmental biology · 2022Article
- The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes.Genes · 2021Review
- Transposable Elements and Stress in Vertebrates: An Overview.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome - the caecilianIchthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.
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