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A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies
Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Alth...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096211/ https://www.ncbi.nlm.nih.gov/pubmed/33511407 http://dx.doi.org/10.1093/nar/gkab010 |
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author | Yu, Tianxiong Huang, Xiao Dou, Shengqian Tang, Xiaolu Luo, Shiqi Theurkauf, William E Lu, Jian Weng, Zhiping |
author_facet | Yu, Tianxiong Huang, Xiao Dou, Shengqian Tang, Xiaolu Luo, Shiqi Theurkauf, William E Lu, Jian Weng, Zhiping |
author_sort | Yu, Tianxiong |
collection | PubMed |
description | Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo ‘singleton’ insertion frequencies in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by de-repressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2. |
format | Online Article Text |
id | pubmed-8096211 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-80962112021-05-10 A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies Yu, Tianxiong Huang, Xiao Dou, Shengqian Tang, Xiaolu Luo, Shiqi Theurkauf, William E Lu, Jian Weng, Zhiping Nucleic Acids Res Methods Online Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo ‘singleton’ insertion frequencies in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by de-repressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2. Oxford University Press 2021-01-28 /pmc/articles/PMC8096211/ /pubmed/33511407 http://dx.doi.org/10.1093/nar/gkab010 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Yu, Tianxiong Huang, Xiao Dou, Shengqian Tang, Xiaolu Luo, Shiqi Theurkauf, William E Lu, Jian Weng, Zhiping A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title | A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title_full | A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title_fullStr | A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title_full_unstemmed | A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title_short | A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
title_sort | benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096211/ https://www.ncbi.nlm.nih.gov/pubmed/33511407 http://dx.doi.org/10.1093/nar/gkab010 |
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