Pan-structural variations in complete plant mitogenomes through a graph-based strategy. Pan-structures of organelle genomes in rice and thale cress

Unlike a typical single-circular structure of most animal mitochondrial genomes and plant chloroplast genomes, the drastic structural variation makes plant mitochondrial genomes as a mixture of molecules in various sizes and structures. To get the full panoramic plant mitochondrial genomes is still considered as the roadblock in evolutionary biology. The current existing plant mitochondrial genome assemblies still lack a systematic strategy for reflecting this diverse structural information. In this study, by combining short reads with high sequence accuracy and long reads with much longer length, we constructed a graph-based sequence assembly toolkit (GSAT) to achieve a high-quality assembly of mitochondrial master graph (MMG) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana), which were able to comprehensively and accurately cover all structural information in the mitochondrial genomes of those two model species.