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Open AccessArticle

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

1
Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
2
Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
3
Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Irina R. Arkhipova
Genes 2021, 12(2), 224; https://doi.org/10.3390/genes12020224
Received: 17 December 2020 / Revised: 30 January 2021 / Accepted: 31 January 2021 / Published: 4 February 2021
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. View Full-Text
Keywords: transposable elements; mobile element insertion events; next-generation sequencing (NGS); genome evolution transposable elements; mobile element insertion events; next-generation sequencing (NGS); genome evolution
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MDPI and ACS Style

Sohrab, V.; López-Díaz, C.; Di Pietro, A.; Ma, L.-J.; Ayhan, D.H. TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. Genes 2021, 12, 224. https://doi.org/10.3390/genes12020224

AMA Style

Sohrab V, López-Díaz C, Di Pietro A, Ma L-J, Ayhan DH. TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. Genes. 2021; 12(2):224. https://doi.org/10.3390/genes12020224

Chicago/Turabian Style

Sohrab, Vista; López-Díaz, Cristina; Di Pietro, Antonio; Ma, Li-Jun; Ayhan, Dilay H. 2021. "TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data" Genes 12, no. 2: 224. https://doi.org/10.3390/genes12020224

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