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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1430443

Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly

Provisionally accepted
Wei Song Wei Song *Chong Li Chong Li *Yanming Lu Yanming Lu Dawei Shen Dawei Shen *Yunxiao Jia Yunxiao Jia *Yixin Huo Yixin Huo Weilan Piao Weilan Piao *Hua Jin Hua Jin *
  • Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China

The final, formatted version of the article will be published soon.

    Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation. To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT). The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow. Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.

    Keywords: Mitochondrial Genome, Chloroplast genome, chromosome-level assembly, organelle identification, horizontal gene transfer

    Received: 09 May 2024; Accepted: 01 Aug 2024.

    Copyright: © 2024 Song, Li, Lu, Shen, Jia, Huo, Piao and Jin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Wei Song, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
    Chong Li, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
    Dawei Shen, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
    Yunxiao Jia, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
    Weilan Piao, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
    Hua Jin, Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.