Experimental conditions improving in-solution target enrichment for ancient DNA

Research output: Contribution to journalJournal articleResearchpeer-review

  • Diana I. Cruz-Dávalos
  • Bastien Llamas
  • Gaunitz, Charleen
  • Antoine Alphonse Fages
  • Cristina Gamba
  • Julien Soubrier
  • Pablo Librado Sanz
  • Andaine Seguin-Orlando
  • Mélanie Pruvost
  • Ahmed H. Alfarhan
  • Saleh A. Alquraishi
  • Khaled A. S. Al-Rasheid
  • Amelie Scheu
  • Norbert Beneke
  • Arne Ludwig
  • Alan Cooper
  • Willerslev, Eske
  • Ludovic Antoine Alexandre Orlando

High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

Original languageEnglish
JournalMolecular Ecology Resources
Issue number3
Pages (from-to)508-522
Number of pages15
Publication statusPublished - May 2017

ID: 172510876