Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers

Accurate phylogenetic analysis of mitochondrial haplotypes underpins a wide spectrum of biological inquiry. While multilocus sequence-based phylogenies are standard, inconsistent gene selection and removal of terminal overhangs during alignment trimming disregard non-coding sequence as well as limit the reproducibility of haplotyping methods. To examine alternative approaches, we tested split k-mer analysis (SKA) to reassess published mitogenome datasets of one mammalian and two insect species. SKA accurately haplotyped each dataset, improved polymorphism detection in the hemipteran Diaphorina citri and aided in the identification of D. citri haplotypes associated with the titer of “Candidatus Liberibacter asiaticus”, the bacterium associated with citrus greening disease. We present a new mitogenome haplotyping method and script, ska-mtdna.py.