ArticleGenome biology and evolution2016
Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
93 citing papers in PubMed, 186 citations in OpenAlex.
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines.Mobile DNA · 2026Article
- Recent Dominant Transposition Events Affect Gene Regulatory Regions, but Not Coding Sequences, in Polar and Brown Bear Genomes.Current issues in molecular biology · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- First reference genome for the family Disteniidae (Coleoptera: Chrysomeloidea), the sister lineage to all longhorned beetles (Cerambycidae).Scientific data · 2026Article
- Genomic resources for two apex avian predators from Saudi Arabia: Falco biarmicus and Falco peregrinus.G3 (Bethesda, Md.) · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- Tetraopes Milkweed Beetle Genomes Elucidate the Adaptive Basis of a Temperate Coevolutionary Radiation.Molecular ecology resources · 2026Article
- Chromosome-Scale Reference Genome Assemblies for Two Anoplophora Longhorned Beetle Species (Coleoptera: Cerambycidae).Genome biology and evolution · 2026Article
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- De novo genome assembly of Ansell's mole-rat (Fukomys anselli).G3 (Bethesda, Md.) · 2026Article
- The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks.Genome biology · 2026Article
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- Characterization of long noncoding RNAs, microRNAs, and piwiRNAs in reef-building corals.Environmental epigenetics · 2026Article
- Chromosome-level genome assembly of the white-spotted sawyer Monochamus scutellatus (Coleoptera: Cerambycidae).Scientific data · 2025Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- Differences in GenBank and RefSeq annotations may affect genomics data interpretation formSphere · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Genomic origins and evolution of neo-sex chromosomes in Pacific Island birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and can occupy more than half of the genome. The increasing number of reference genomes from nonmodel species has begun to outpace efforts to identify and annotate TE content and methods that are used vary significantly between projects. Here, we demonstrate variation that arises in TE annotations when less than optimal methods are used. We found that across a variety of taxa, the ability to accurately identify TEs based solely on homology decreased as the phylogenetic distance between the queried genome and a reference increased. Next we annotated repeats using homology alone, as is often the case in new genome analyses, and a combination of homology and de novo methods as well as an additional manual curation step. Reannotation using these methods identified a substantial number of new TE subfamilies in previously characterized genomes, recognized a higher proportion of the genome as repetitive, and decreased the average genetic distance within TE families, implying recent TE accumulation. Finally, these finding-increased recognition of younger TEs-were confirmed via an analysis of the postman butterfly (Heliconius melpomene). These observations imply that complete TE annotation relies on a combination of homology and de novo-based repeat identification, manual curation, and classification and that relying on simple, homology-based methods is insufficient to accurately describe the TE landscape of a newly sequenced genome.
Indexed as
Identifiers
What OpenQuestion holds
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.