Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework

文献类型： 外文期刊

第一作者： He, Wenchuang

作者： He, Wenchuang;Xiang, Kunli;Wang, Jie;Wu, Zhiqiang;Chen, Caijin;Wu, Zhiqiang

作者机构：

关键词： Graph-based mitochondrial genome; mitochondrial master graph; pan-structure; Oryza sativa; Arabidopsis thaliana

期刊名称：BRIEFINGS IN BIOINFORMATICS （ 影响因子：9.5； 五年影响因子：10.6 ）

ISSN： 1467-5463

年卷期： 2022 年

页码：

收录情况： SCI

摘要： Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.

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