ArticleMolecular biology and evolution2016
Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.
Article in Molecular biology and evolution, 2016. 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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19 citing papers in PubMed, 43 citations in OpenAlex.
- ThePlants (Basel, Switzerland) · 2026Review
- Genome-Wide Analysis of theInternational journal of molecular sciences · 2026Article
- Genome-Wide Identification and Expression Analysis of the FAR1-RELATED SEQUENCE (FRS) Gene Family in Grape (International journal of molecular sciences · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Genome-wide analysis of FRF gene family and functional identification ofFrontiers in plant science · 2024Article
- The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity.bioRxiv : the preprint server for biology · 2023Article
- Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature.Plant physiology · 2023Article
- Review
- Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution.Mobile DNA · 2021Article
- Review
- Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes.Molecular biology and evolution · 2021Article
- Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae.G3 (Bethesda, Md.) · 2020Article
- Telomeric TART elements target the piRNA machinery in Drosophila.PLoS biology · 2020Article
- Halophytism: What Have We Learnt FromPlant physiology · 2018Review
- Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana.Genome biology and evolution · 2018Article
- FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) Family Proteins inFrontiers in plant science · 2018Review
- Transposable Element Domestication As an Adaptation to Evolutionary Conflicts.Trends in genetics : TIG · 2017Review
- Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication.Genome biology and evolution · 2017Article
- Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements.Frontiers in plant science · 2017Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution.
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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.