2021

Molecular Ecology Resources

Rocznik: 2021 | Tom: on-line

artykuł naukowy

angielski

EN DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analys ing ancient DNA (aDNA) extracts, which are often dominated by exogenous environ mental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic re striction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA li braries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing ex tremely low endogenous content (20%–30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensi tive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypo methylated regions, which improved data quality by reducing post-mortem DNA dam age and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture process ing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.

28.09.2021

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10.1111/1755-0998.13518

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13518

CC BY-NC-ND (uznanie autorstwa - użycie niekomercyjne - bez utworów zależnych)

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28.09.2021

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