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

Inconsistent gene selection and trimming are weaknesses in generation of reproducible multilocus sequence type (MLST) phylogenies. As an alternative, we tested split k -mer analysis (SKA), which uses short, fixed-length nucleotide sequences, to haplotype mitogenomes of three animal species. SKA accurately haplotyped each species and exceeded MLST sensitivity for the Asian citrus psyllid by identifying haplotypes associated with Candidatus Liberibacter asiaticus titer, revealing new information on the genetic basis of vector competence in an economically important insect.