Related Experiment Video
Updated: Nov 17, 2025
06:59
Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
Published on: March 31, 2022
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Third-generation sequencing-based mapping and visualization of single nucleotide polymorphism, meiotic recombination,
Wan-Chen Li1, Hou-Cheng Liu1, Ying-Jyun Lin1
1Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
NAR Genomics and Bioinformatics
|February 12, 2021
Summary
We developed TSETA, a new pipeline for mapping genetic recombination and mutation in fungi. This tool aids in understanding genome evolution and identifying genetic variations across species.
Area of Science:
- Genetics
- Molecular Biology
- Mycology
Background:
- Genetic diversity arises from crossover (CO), non-crossover (NCO), illegitimate mutation (IM), and repeat-induced point mutation (RIP).
- Fungi are crucial models for studying meiotic recombination due to tetrad analysis capabilities.
- Repeat-induced point mutation (RIP) is a fungal genome defense mechanism against transposable elements, potentially involving DNA methylation.
Purpose of the Study:
- To develop a comprehensive method for high-throughput mapping of CO, NCO, RIP, and IM in fungal zygotes.
- To enable a deeper understanding of the molecular mechanisms driving genetic variation and genome evolution.
- To provide a versatile tool applicable to most sexual eukaryotes for genome-wide tetrad analysis.
Main Methods:
- Development of 'TSETA', a user-friendly bioinformatics pipeline.
- Utilizing high-quality, chromosome-level genome sequences from *Trichoderma reesei* meiotic events.
- High-throughput mapping of recombination and mutation events using heterozygous variant markers.
Main Results:
- TSETA enables precise genome-wide tetrad analysis in sexual eukaryotes.
- The pipeline effectively maps crossover (CO), non-crossover (NCO), illegitimate mutation (IM), and repeat-induced point mutation (RIP) events.
- TSETA surpasses existing methods for single nucleotide polymorphism (SNP) calling between intraspecies strains.
Conclusions:
- TSETA is a versatile and efficient tool for studying genetic variation and meiotic recombination.
- The pipeline facilitates research into genome evolution and defense mechanisms across eukaryotes.
- TSETA offers improved SNP detection capabilities for intraspecies comparisons.
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