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Updated: Jun 3, 2025
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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
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Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies
Yan Huang1,2,3, Sunil Kumar Sahu1,2, Xin Liu1,2,3
1College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Plant Biotechnology Journal
|January 10, 2025
Summary
Transposable elements (TEs) drive genome evolution. This study reveals their dynamics, host gene interactions, and impact on plant adaptation and crop domestication.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Science
Background:
- Transposable elements (TEs) significantly influence genome evolution, but their recent dynamics and interactions with host factors are not fully understood.
- Host genes and non-coding RNAs (ncRNAs) may play roles in TE transposition, impacting chromatin regulation.
Purpose of the Study:
- To comprehensively analyze transposable element (TE) dynamics and their evolutionary impacts across diverse plant species.
- To investigate the interplay between TEs, host genes, and ncRNAs in transposition and genome evolution.
- To elucidate the role of TEs in plant adaptation and crop domestication.
Main Methods:
- Performed de novo TE annotations and identified active TEs in 310 plant genome assemblies (119 species).
- Detected 13,844,553 TE-induced structural variants (TE-SVs) using 811 high-quality genomes.
- Conducted integrative analysis of TE-host genome relationships, including colocalization and coactivation patterns.
Main Results:
- Identified a mutual evolutionary relationship between TEs and host genomes.
- Demonstrated host gene and ncRNA involvement in TE transposition and chromatin regulation.
- Showcased TEs driving genetic innovation through gene duplication and regulatory region insertion.
- Linked genes influenced by active TEs to plant growth, nutrient uptake, metabolism, and adaptation.
Conclusions:
- TEs are crucial drivers of genetic innovation and adaptation in plants.
- Active TEs influence traits vital for crop domestication and improvement.
- This TE dynamics atlas provides insights into TE-mediated genome evolution and strategies for crop enhancement.
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