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Oatk: a de novo assembly tool for complex plant organelle genomes
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Oatk: a de novo assembly tool for complex plant organelle genomes
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Journal Article
Oatk: a de novo assembly tool for complex plant organelle genomes
2025
Overview
Plant organelle genomes, particularly large mitochondrial genomes with complex repeats, present significant challenges for assembly. The advent of long-read sequencing enables the assembly of complete genomes, but problems of resolving alternative structures remain. Here we introduce a novel tool that employs a syncmer-based assembler for rapid assembly graph construction, integrates a profile-HMM database for robust organelle identification, 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, demonstrating improvements over other methods, and providing multiple insights into structural complexity, heteroplasmy, and DNA exchange between organelles.
Publisher
BioMed Central,Springer Nature B.V,BMC
Subject
/ Biomedical and Life Sciences
/ DNA
/ Genomes
/ Microbial Genetics and Genomics
/ Plastome
/ Seeds
/ Software
/ species
/ Syncmer
