Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA

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Authors

ŠENOVSKÁ Anna DROZDOVÁ Eva VACULÍK Ondřej PARDY Filip BRZOBOHATÁ Kristýna FIALOVÁ Dana ŠMERDA Jaromír KOS Petr

Year of publication 2021
Type Article in Periodical
Magazine / Source Forensic Science International
MU Faculty or unit

Faculty of Science

Citation
Web https://doi.org/10.1016/j.forsciint.2020.110638
Doi http://dx.doi.org/10.1016/j.forsciint.2020.110638
Keywords Ancient DNA; Mitochondrial DNA; Mitogenome; Capture; Enrichment; Sequencing
Description Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.
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