TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Transposable elements (TEs) are mobile genetic sequences driving genome evolution and genetic instability.
• Existing bioinformatics tools for TE insertion detection often have limitations like narrow focus or complex dependencies.
• Accurate identification of TEs is crucial for understanding their role in biological processes.

Purpose of the Study:

• To develop a user-friendly bioinformatics pipeline for detecting new transposable element insertions.
• To minimize software and input file dependencies for broader accessibility.
• To provide a practical tool for analyzing TE dynamics in evolving populations.

Main Methods:

• Developed TEfinder, a pipeline requiring minimal external software (BEDTools, SAMtools, Picard).
• Input requirements include reference genome (FASTA), paired-end read alignment (BAM/SAM), existing TEs (GTF), and TE names (TXT).
• Tested TEfinder on evolving populations of *Fusarium oxysporum* from a short-term adaptation study.

Main Results:

• TEfinder effectively detected new transposable element insertion events.
• The tool demonstrated ease of use and practicality in analyzing TE insertions.
• Successful application in identifying TE dynamics within experimental populations.

Conclusions:

• TEfinder offers a simplified and accessible approach to detecting transposable element insertions.
• The pipeline's minimal dependencies make it a practical choice for researchers.
• This tool facilitates the study of genome evolution and genetic variation driven by TEs.