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Updated: Mar 12, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
Recent and dynamic transposable elements contribute to genomic divergence under asexuality.
Julie Ferreira de Carvalho1, Victor de Jager2, Thomas P van Gurp3
1Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands. j.ferreiradecarvalho@nioo.knaw.nl.
Transposable elements (TEs) drive genome evolution in asexual dandelions. Accession-specific TEs show variable transcription and methylation, potentially altering nearby gene expression and promoting adaptive variation.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Science
Background:
- Transposable elements (TEs) are mobile genetic sequences with mutagenic potential.
- Their role in asexual plant genome evolution is understudied.
- This study investigates TEs in the asexual common dandelion (Taraxacum officinale).
Purpose of the Study:
- To characterize the repetitive fraction of the T. officinale genome.
- To evaluate TE content and activity within an asexual lineage.
- To identify accession-specific TEs and their epigenetic variations.
Main Methods:
- Low-coverage genomic sequencing to analyze TE compartment.
- Analysis of repeat cluster identity for recent TE activity.
- Reduced representation bisulfite sequencing for DNA methylation analysis.
- Differential transcription analysis of TEs.
Main Results:
- The T. officinale genome contains a highly heterogeneous TE compartment (up to 38.6%).
- LTR retrotransposons dominate the repetitive fraction, with evidence of recent TE activity.
- Five accessions clustered into two clades based on TE composition, with Clade 2 being more dynamic.
- Accession-specific TEs were identified with differential transcription and methylation, including LTR and DNA transposons.
- 18.9% of loci showed differential methylation, with TEs and genes being significantly represented.
Conclusions:
- A young and dynamic TE compartment enhances divergence within the asexual T. officinale lineage.
- Transcriptionally and epigenetically variable TEs may influence nearby coding sequences.
- TE-induced mutations offer a significant source of functional variation in asexual plant evolution.
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