ReviewMolecular phylogenetics and evolution2015
A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.
Review in Molecular phylogenetics and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
76 citing papers in PubMed, 161 citations in OpenAlex.
- Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates.Genome biology and evolution · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2.Biology · 2025Article
- The Other Side of the Same Coin: Beyond the Coding Region in Amyotrophic Lateral Sclerosis.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Aging-Related Mechanisms Underlying Carcinogenesis: Therapeutic Opportunities.Aging and disease · 2025Review
- Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot.Journal of applied genetics · 2025Article
- LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression.Genome biology · 2025Article
- Article
- A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity.Nucleic acids research · 2024Article
- FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research.Database : the journal of biological databases and curation · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.Cell host & microbe · 2024Article
- Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.bioRxiv : the preprint server for biology · 2024Article
- Article
- Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges.Genome research · 2023Article
- From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution.Functional & integrative genomics · 2023Review
- Comparative genomics reveals insights into anuran genome size evolution.BMC genomics · 2023Article
- Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Transposable Elements Co-Option in Genome Evolution and Gene Regulation.International journal of molecular sciences · 2023Review
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).
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Registered trials
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.