期刊
GENES
卷 12, 期 2, 页码 -出版社
MDPI
DOI: 10.3390/genes12020224
关键词
transposable elements; mobile element insertion events; next-generation sequencing (NGS); genome evolution
资金
- University of Massachusetts Amherst Honors College Research grant
- National Institute of Health [R01EY030150]
- Burroughs Welcome Foundation [1014893]
- FEDER Junta de Andalucia [27374-R]
- United States Department of Agriculture, National Institute of Food and Agriculture [2011-35600-30379, MASR-2009-04374]
- National Science Foundation [IOS-1652641]
- Spanish Ministerio de Ciencia e Innovacion MICINN [PID2019-108045RB-I00]
TEfinder is a simple tool developed for the detection of new TE insertions with minimal software and input file dependencies. The tool has been tested in evolving populations of Fusarium oxysporum and shown to effectively detect new TE insertion events, making it accessible and practical for TE analysis.
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据