Zhang Panpan, Peng Haoran, Llauro Christel, Bucher Etienne, Mirouze Marie
Institut de Recherche pour le Développement (IRD), Montpellier, France.
Laboratory of Plant Genome and Development, University of Perpignan, Perpignan, France.
Front Plant Sci. 2021 Dec 1;12:743742. doi: 10.3389/fpls.2021.743742. eCollection 2021.
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. Applying ecc_finder to eccDNA-seq data (either mobilome-seq, Circle-Seq and CIDER-seq) from , 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.
几十年来，人们在不同物种中都观察到了染色体外环状DNA（eccDNA），越来越多的证据表明，这种特定类型的DNA分子可能在快速适应中发挥重要作用。因此，描绘eccDNA的全貌变得至关重要，目前有几种用于富集eccDNA并进行短读长或长读长测序的方案。然而，目前还没有可用的生物信息学工具从纳米孔读数中识别eccDNA。更重要的是，目前基于Illumina短读长的工具缺乏一个高效的标准化流程，尤其是无法识别来自重复位点的eccDNA，并且不能应用于非常大的基因组。在这里，我们介绍一种综合工具来解决这两个问题。将ecc_finder应用于来自人、小麦（基因组大小从120Mb到17Gb不等）的eccDNA序列数据（包括转座因子测序、Circle-Seq和CIDER-Seq），我们记录了计算时间、灵敏度和准确性的提升，并证明了ecc_finder的广泛适用性和功能。
