ArticlePLoS genetics2021
The genomic ecosystem of transposable elements in maize.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed, 138 citations in OpenAlex.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
- Constitutive and tissue-specific target site preferences of the maize Mutator transposon.bioRxiv : the preprint server for biology · 2026Article
- High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance.Scientific data · 2026Article
- Transposon Ecology and the Octopus Genome.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus.Scientific reports · 2026Article
- The evolutionary genomics of meiotic drive.Molecular biology and evolution · 2026Article
- MaizeGDB Phylostrata Tool: exploring evolutionary origins of maize proteins.Bioinformatics advances · 2026Article
- A Pan-TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Transposable elements: a key piece in the genomic evolution and adaptation of Myrtaceae species.Mobile DNA · 2025Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- A comparative analysis of transposable element diversity and evolution across 75 bee genomes.BMC genomics · 2025Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).Genome biology · 2025Article
- Integration of Repeatome and Cytogenetic Data on Tandem DNAs in a Medicinal PlantInternational journal of molecular sciences · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Beautiful and delicious mutants: The origins, fates, and benefits of molecular sequence variation in plant evolution and breeding.Plant physiology · 2025Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
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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.