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Updated: Jul 9, 2026
04:04
Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
TEnest: automated chronological annotation and visualization of nested plant transposable elements
Brent A Kronmiller1, Roger P Wise
1Bioinformatics and Computational Biology, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, IA 50011-1020, USA.
Plant Physiology
|November 23, 2007
Summary
TEnest is a new tool for analyzing transposable elements (TEs) in complex genomes. It reconstructs nested repeats and visualizes TE history, revealing insights into genome evolution, particularly in maize.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- High transposable element (TE) density in genomes leads to nested structures, complicating repeat annotation.
- Understanding TE dynamics is crucial for deciphering genome evolution and structure.
Purpose of the Study:
- To introduce TEnest, a novel computational tool for identifying and visualizing repetitive sequences in highly repetitive genomes.
- To reconstruct fragmented transposable elements and analyze their insertion history and evolutionary relationships.
Main Methods:
- Development of the TEnest software for repeat identification and reconstruction.
- Application of TEnest to analyze transposable elements in maize, rice, wheat, and barley genomes.
- Calculation of insertion ages for long-terminal repeat (LTR) retrotransposons based on LTR divergence.
Main Results:
- TEnest successfully identifies and reconstructs nested TEs, providing full-length repeat information.
- Analysis of maize genomes revealed TEs constitute 67% of the genome, with 95% being LTR retrotransposons.
- Disparate solo LTR formation rates and phylogenetic analysis indicated specific TE proliferation events in maize.
Conclusions:
- TEnest offers a robust framework for visualizing TE integration history and facilitating evolutionary comparisons.
- The study provides a comprehensive characterization of repeat insertions in maize, highlighting significant TE activity.
- TEnest is a valuable resource for studying repetitive genomes and understanding transposable element evolution.
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