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

Vista Sohrab,Dilay Hazal Ayhan,Cristina López-Díaz,Antonio Di Pietro,Li-Jun Ma

doi:10.3390/genes12020224

Vista Sohrab, Dilay Hazal Ayhan + Show 3 more

Open Access

https://doi.org/10.3390/genes12020224

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Abstract

Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.

Highlights

Transposable elements (TEs) are DNA sequences that move from one genomic location to another and impact genome evolution and organism adaptation [1]
Encountering difficulties in applying available TE insertion detection tools, we developed a simple bash bioinformatics pipeline, TEfinder, to detect new insertion events using tools that are commonly embedded in genomics variant calling workflows, including
We report the design of the pipeline, testing results of its performance using short-read sequencing data derived from a short-term evolution experiment in the filamentous fungus Fusarium oxysporum f. sp. lycopersici 4287 (Fol4287), as well as a simulation dataset from chromosome 2 L of Drosophila melanogaster [16], and two datasets from the Arabidopsis thaliana mobilome study [17,18]

Summary

Introduction

Transposable elements (TEs) are DNA sequences that move from one genomic location to another and impact genome evolution and organism adaptation [1]. TE transposition can alter the genomic architecture, introduce structural polymorphisms, disrupt coding sequences, and affect transcriptional and translational regulation. TEs provide a wide array of genomic diversity, functional impact, and evolutionary consequences that can be of notable interest to population genetics, host interaction, and comparative genomics studies. TEs comprise a significant portion of the genome of humans and many other organisms, due to their mobilization and accumulation throughout evolution [4]. While some TEs are no longer active, certain TE families remain mobile and their transposition contributes to genetic variation both at the individual and the population level.

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