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

Authors: KNEUBEHL, ALEXANDER - Baylor College Of Medicine; MUNOZ LEAL, SEBASTIAN - University Of Concepcion; FILATOV, SERHII - Baylor College Of Medicine; BERMUDEZ, SERGIO - Gorgas Memorial Institute Of Health Studies; EISEN, REBECCA - Centers For Disease Control And Prevention (CDC) - United States; Perez De Leon, Adalberto - Beto; Lohmeyer, Kimberly - Kim; TEEL, PETE - Texas Agrilife Research; LABRUNA, MARCELO - Universidad De Sao Paulo; MANS, BENS - University Of Pretoria; LOPEZ, JOB - Baylor College Of Medicine

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2022
Publication Date: 11/11/2022
Citation: Kneubehl, A.R., Munoz Leal, S., Filatov, S., Bermudez, S.E., Eisen, R.J., Perez De Leon, A.A., Lohmeyer, K.H., Teel, P.D., Labruna, M.B., Mans, B.J., Lopez, J.E. 2022. Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis. Scientific Reports. https://doi.org/10.1038/s41598-022-23393-5.
DOI: https://doi.org/10.1038/s41598-022-23393-5

Interpretive Summary: Ticks are important external parasites because they bite and feed on the blood of livestock, wildlife, and humans. Several tick species also transmit diverse microbes that cause diseases. The mitochondrion is a structure within cells that a nucleus where energy is produced through the process of cellular respiration. Mitogenome is the suite of genes in the mitochondrion. Sequencing the mitogenome is important to understand the relationship of tick species and the genetics of population structure. However, obtaining the sequence of tick mitogenomes can be expensive. A cost-effective approach for amplifying and sequence the whole mitogenome of individual tick specimens was developed through the research described herein. Adaptation of next-generation sequencing methods yielded 85 individual tick mitogenomes from samples comprising 57 species. Twenty-four of these species did not have a complete mitogenome entry in the publicly available database GenBank prior to this work. These novel assemblies were comparable or exceeded results obtained with a previously validated method. This cost-effective (cost/sample of ~$10 USD) strategy is applicable for research not only ticks but likely other multi-cellular organisms. Our novel approach makes mitogenome sequencing equitable for the wider scientific community.

Technical Abstract: 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 for amplifying and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generates 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-four 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 Illumina genome skimming. We found our assemblies to be 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 74 samples at one time 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.