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bioRxiv · 10.1101/2024.10.23.619857

Oatk: a de novo assembly tool for complex plant organelle genomes

Zhou, C.·Brown, M.·Blaxter, M.·The Darwin Tree of Life Project Consortium,·McCarthy, S. A.·Durbin, R.
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Abstract

Plant organelle genomes, particularly the large mitochondrial genomes with intricate repetitive structures, present significant challenges for assembly. The advent of long-read sequencing technologies provides a transformative opportunity to generate complete genomes, but problems of resolving alternative structures remain. Here we introduce a novel tool for plant organelle genome assembly from high-accuracy long reads. Our method employs a k-mer based assembler for rapid assembly graph construction, integrates a profile HMM gene database for robust organelle sequence annotation, and leverages a new search method to find the best supported path through the assembly graph. We describe high-quality organelle assemblies for 195 plant species and demonstrate improvements over other methods. The assembled genomes provide multiple insights into structural complexity, heteroplasmy, and DNA exchange between organelles.

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Zhou, C., Brown, M., Blaxter, M., The Darwin Tree of Life Project Consortium,, McCarthy, S. A., Durbin, R.. 2024-10-28. Oatk: a de novo assembly tool for complex plant organelle genomes. https://doi.org/10.1101/2024.10.23.619857

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