ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data

Extrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this specific type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there a...

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Autores principales:	Panpan Zhang, Haoran Peng, Christel Llauro, Etienne Bucher, Marie Mirouze
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	eccDNA nanopore amplicon sequencing mobilome Arabidopsis wheat Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/ea57395139c849799057bd62f2109b4d
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spelling	oai:doaj.org-article:ea57395139c849799057bd62f2109b4d2021-12-02T00:37:35Zecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data1664-462X10.3389/fpls.2021.743742https://doaj.org/article/ea57395139c849799057bd62f2109b4d2021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.743742/fullhttps://doaj.org/toc/1664-462XExtrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this specific type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there are several protocols for enriching eccDNAs and performing short-read or long-read sequencing. However, there is currently no available bioinformatic tool to identify eccDNAs from Nanopore reads. More importantly, the current tools based on Illumina short reads lack an efficient standardized pipeline notably to identify eccDNA originating from repeated loci and cannot be applied to very large genomes. Here, we introduce a comprehensive tool to solve both of these two issues.1 Applying ecc_finder to eccDNA-seq data (either mobilome-seq, Circle-Seq and CIDER-seq) from Arabidopsis, human, and wheat (with genome sizes ranging from 120Mb to 17 Gb), we document the improvement of computational time, sensitivity, and accuracy and demonstrate ecc_finder wide applicability and functionality.Panpan ZhangPanpan ZhangHaoran PengHaoran PengChristel LlauroChristel LlauroEtienne BucherMarie MirouzeMarie MirouzeFrontiers Media S.A.articleeccDNAnanopore amplicon sequencingmobilomeArabidopsiswheatPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	eccDNA nanopore amplicon sequencing mobilome Arabidopsis wheat Plant culture SB1-1110
spellingShingle	eccDNA nanopore amplicon sequencing mobilome Arabidopsis wheat Plant culture SB1-1110 Panpan Zhang Panpan Zhang Haoran Peng Haoran Peng Christel Llauro Christel Llauro Etienne Bucher Marie Mirouze Marie Mirouze ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
description	Extrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this specific type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there are several protocols for enriching eccDNAs and performing short-read or long-read sequencing. However, there is currently no available bioinformatic tool to identify eccDNAs from Nanopore reads. More importantly, the current tools based on Illumina short reads lack an efficient standardized pipeline notably to identify eccDNA originating from repeated loci and cannot be applied to very large genomes. Here, we introduce a comprehensive tool to solve both of these two issues.1 Applying ecc_finder to eccDNA-seq data (either mobilome-seq, Circle-Seq and CIDER-seq) from Arabidopsis, human, and wheat (with genome sizes ranging from 120Mb to 17 Gb), we document the improvement of computational time, sensitivity, and accuracy and demonstrate ecc_finder wide applicability and functionality.
format	article
author	Panpan Zhang Panpan Zhang Haoran Peng Haoran Peng Christel Llauro Christel Llauro Etienne Bucher Marie Mirouze Marie Mirouze
author_facet	Panpan Zhang Panpan Zhang Haoran Peng Haoran Peng Christel Llauro Christel Llauro Etienne Bucher Marie Mirouze Marie Mirouze
author_sort	Panpan Zhang
title	ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
title_short	ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
title_full	ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
title_fullStr	ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
title_full_unstemmed	ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
title_sort	ecc_finder: a robust and accurate tool for detecting extrachromosomal circular dna from sequencing data
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/ea57395139c849799057bd62f2109b4d
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ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data

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