An additional strategy is amplification and sequencing of the mitogenome in multiple amplicons 12, 17, 18, 19. Current strategies to sequence tick mitogenomes largely revolve around genome skimming, which is low-coverage sequencing of a genomic DNA sample and recovering reads to completely assemble both the mitogenome and nuclear loci 10, 11, 13, 14, 15, 16. Advances in mitogenome sequencing of individual tick specimens pushed tick taxonomy and systematics to new heights in the last few years 10, 11, 12, 13, and have expanded our ability to perform population genetics studies to investigate tick dispersal and distribution 13, 14. The abundance of the mitogenome allows for easier amplification or direct sequencing from degraded samples 8, 9. The mitogenome has great utility for molecular analyses as it is haploid, does not undergo recombination, and exists in greater abundance relative to the nuclear genome 7.
One approach to investigate tick dispersal is through analysis of mitochondrial genomes (mitogenomes). Given the health concerns associated with these arthropods, surveillance and investigations into mechanisms of dispersal are necessary. Furthermore, tick bites are capable of eliciting a variety of acute and long-term conditions, not caused by an infectious agent, such as tick toxicosis 3, 4, 5 and alpha-gal syndrome (red meat allergy) 6. Ticks (Acari: Ixodida) comprise over 900 species of obligate hematophagous arthropods many of which are important vectors of pathogens for both humans and livestock 1, 2.
This cost-effective strategy is applicable for sample identification, taxonomy, systematics, and population genetics for not only ticks but likely other metazoans thus, making mitogenome sequencing equitable for the wider scientific community. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies’ Mk1B sequencer. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. However, current methods to generate mitogenomes can be cost-prohibitive at scale.
The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks.
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