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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- Department of Biological Sciences, School of Life Sciences, Beijing Institute of Technology, Zhongguancun, China
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
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