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

Douglas S Stuehler, Liliana M Cano, Michelle Heck

Abstract read

In one paragraph

Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Douglas S StuehlerOak Ridge Institute for Science and Education, USDA Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, NY, 14853, USA.

Liliana M CanoIndian River Research and Education Center, Department of Plant Pathology, Institute of Food and Agriculture Sciences, University of Florida, Fort Pierce, FL, 34945, USA.

Michelle HeckSection of Plant Pathology and Plant Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. michelle.heck@usda.gov.

Funding

Agricultural Research Service 8062-22410-007-000-DEmergency Citrus Disease Research and Extension Program 2020-70029-33176National Institute of Food and Agriculture 2022-70029-038503

6 · The paper itself

Abstract

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.

Indexed as

Genome, MitochondrialHaplotypesAnimalsHemipteraPhylogenyReproducibility of ResultsAsian citrus psyllidCryptic speciesDiaphorina citriHaplotype networkHaplotypingHuanglongbingLiberibacterMitochondriaMulti-locus sequence typingSplit k-mer

Identifiers

PMID41963795

DOI10.1186/s12864-026-12811-x

PMCPMC13181888

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.