■准确的参考基因组是理解生物进化的基础,生物多样性,遗传现象和疾病。然而,许多组装的核染色体经常被细胞器基因组污染,这会误导生物信息学分析,以及基因组和转录组数据解释。
■要解决此问题,我们开发了一个名为Chlomito的工具,旨在精确识别和消除核基因组组装中的细胞器基因组污染。与传统方法相比,Chlomito利用了新的指标,比对长度覆盖率(ALCR)和测序深度比(SDR),从而有效区分真正的细胞器基因组序列与通过水平基因转移(HGT)转移到核基因组中的那些。
■使用来自Plum的测序数据测试了Chlomito的准确性,芒果和拟南芥。结果证实,Chlomito可以准确地检测出源自细胞器基因组的重叠群,识别出的重叠群覆盖了细胞器参考基因组的大部分区域,演示Chlomito的效率和精度。考虑到用户的便利性,我们进一步将此方法打包到Docker映像中,简化了数据处理工作流程。
■总的来说,Chlomito提供了一种高效的,在基因组组装数据中识别和去除源自细胞器基因组的重叠群的准确和方便的方法,有助于提高基因组组装质量。
UNASSIGNED: 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.
UNASSIGNED: 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).
UNASSIGNED: 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.
UNASSIGNED: 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.