DoveTailor: a path-preserving assembler for dynamic mitochondrial genomes

Introduction: Multipartite mitochondrial genomes often consist of multiple conformations that pose a challenge for conventional genome assembly tools, particularly in the presence of recombination and low-abundance isoforms. Materials and methods: The primary objective of this work is to introduce DoveTailor, a path-preserving assembler designed to assemble all isoforms of multipartite plant mitochondrial genomes, and compare the validity of its assemblies to two popular assembly tools. DoveTailor builds a read-to-read connectivity map, explores all extension paths, and uses k-mer-based equivalence to collapse redundant assemblies. We applied DoveTailor to mitochondrial genomes of Tylosema esculentum (Types I and II) and Linum usitatissimum and compared the results to assemblies generated by Flye and Organelle Assembly ToolKit (OATK). Results: DoveTailor assemblies of Type I and Type II T. esculentum resolve the full set of unique genetic material in addition to recombination-derived isoforms verified by long-read and short-read alignments. Conventional assemblers fail to capture either the full set of material or genomic structures. Conclusions: DoveTailor provides an effective approach for assembling isoform-rich, non-linear DNA structures and enables more complete characterization of plant mitochondrial genome organization, while remaining as a standalone application with a graphical user interface (GUI) which requires no command-line experience.