Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis

• Published in: Scientific reports Vol. 12; no. 1; p. 19310
• Main Authors: Kneubehl, Alexander R., Muñoz-Leal, Sebastián, Filatov, Serhii, de Klerk, Daniel G., Pienaar, Ronel, Lohmeyer, Kimberly H., Bermúdez, Sergio E., Suriyamongkol, Thanchira, Mali, Ivana, Kanduma, Esther, Latif, Abdalla A., Sarih, M’hammed, Bouattour, Ali, de León, Adalberto A. Pérez, Teel, Pete D., Labruna, Marcelo B., Mans, Ben J., Lopez, Job E.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11.11.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/2217/457; 631/1647/2217/748; 631/1647/48; 631/1647/514/1948; 631/181/2480; 631/181/457; 631/181/757; 631/208; 631/208/212/748; 631/208/2156; 631/601/1466; Animals; Arachnids; Genera; Genetics; Genome, Mitochondrial - genetics; Genomes; Genomic analysis; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Humans; Mitochondria; multidisciplinary; Phylogeny; Population genetics; Science; Science (multidisciplinary); Sequence Analysis, DNA; Systematics; Taxonomy; Ticks - genetics
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-23393-5

The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks. However, current methods to generate mitogenomes can be cost-prohibitive at scale. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies’ Mk1B sequencer. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. 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.