Performance and automation of ancient DNA capture with RNA hyRAD probes

• DOI: 10.1111/1755-0998.13518
• Publication Date: 2021-09-28T21:20:34Z
• Authors: Tomasz Suchan; Mariya A. Kusliy; Naveed Khan; Loreleï Chauvey; Laure Tonasso‐Cal...; Stéphanie Schiavi...; John Southon; Marcel Keller; Keiko Kitagawa; Johannes Krause; Alexander N. Bess...; Alexander A. Bess...; Alexander S. Grap...; Silvia Valenzuela...; Jarosław Wilczyński; Sylwia Pospuła; Krzysztof Tunia; Marek Nowak; Magdalena Moskal‐...; Alexey A. Tishkin; Alexander J. E. P...; Alan K. Outram; Ludovic Orlando
• Keywords: Ancient DNA; genomic DNA

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, performance of hyRAD as an inexpensive and design-free alternative commercial capture protocols obtain authentic aDNA data from osseous remains. HyRAD relies double enzymatic restriction fresh extracts produce RNA probes that cover only a fraction genome can serve baits capturing homologous fragments libraries. We found this approach could retrieve sequence horse remains coming range preservation environments, including beyond radiocarbon range, yielding up 146.5-fold on-target enrichment showing extremely low endogenous content (<1%). Performance was, however, more limited those samples already characterized good (>20%-30%), while reads mapping on- off-target was relatively insensitive original content. Procedures based two instead single round increased coverage 3.6-fold. Additionally, used methylation-sensitive enzymes targeting hypomethylated regions, improved quality reducing post-mortem damage within multicopy Finally, developed fully automated protocol utilizing robotic platforms facilitate processing. Overall, our work establishes cost-effective strategy recover set shared orthologous variants across multiple samples.