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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
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ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data
Panpan Zhang1,2, Haoran Peng3,4, Christel Llauro2,5
1Institut de Recherche pour le Développement (IRD), Montpellier, France.
Frontiers in Plant Science
|December 20, 2021
Summary
A new tool, ecc_finder, identifies extrachromosomal circular DNA (eccDNA) from Nanopore sequencing and improves analysis of short-read data, especially for large genomes and repetitive regions.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
- Evolutionary Biology
Background:
- Extrachromosomal circular DNA (eccDNA) molecules are increasingly recognized for their role in rapid adaptation across species.
- Existing sequencing protocols can enrich eccDNA, but bioinformatic tools for analysis, particularly from Nanopore data and large genomes, are lacking.
- Current short-read analysis tools struggle with identifying eccDNA from repetitive genomic loci and are inefficient for massive genomes.
Purpose of the Study:
- To develop a comprehensive bioinformatic tool, ecc_finder, for identifying eccDNA from both Nanopore and short-read sequencing data.
- To address limitations in current tools regarding Nanopore read analysis, large genome applicability, and identification of eccDNA from repetitive regions.
- To provide an efficient and standardized pipeline for eccDNA landscape characterization.
Main Methods:
- Development and application of the ecc_finder bioinformatic tool.
- Analysis of eccDNA-seq data (mobilome-seq, Circle-Seq, CIDER-seq) from diverse species including *Arabidopsis*, human, and wheat.
- Evaluation of ecc_finder's performance on genomes ranging from 120Mb to 17Gb.
Main Results:
- ecc_finder demonstrates significant improvements in computational time, sensitivity, and accuracy compared to existing methods.
- The tool successfully identifies eccDNA from Nanopore sequencing reads, filling a critical gap in current bioinformatic capabilities.
- ecc_finder effectively analyzes eccDNA from large genomes and repetitive loci, showcasing its wide applicability and functionality across different species and genome sizes.
Conclusions:
- ecc_finder provides a robust and versatile solution for characterizing the eccDNA landscape using various sequencing technologies.
- This tool enhances the ability to study the role of eccDNA in biological processes, including rapid adaptation.
- The development of ecc_finder represents a significant advancement in the field of eccDNA research, enabling more comprehensive genomic analyses.
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