title: Experimental conditions improving in-solution target enrichment for ancient DNA.
abstract: 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.
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.|Undergraduate Program on Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, 62210, Cuernavaca, Mexico.
authors: Diana I
authors: DI
authors: Cruz-Dávalos
authors: Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
authors: Bastien
authors: B
authors: Llamas
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors: Charleen
authors: C
authors: Gaunitz
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.|Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, 31000, Toulouse, France.
authors: Antoine
authors: A
authors: Fages
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors: Cristina
authors: C
authors: Gamba
authors: Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
authors: Julien
authors: J
authors: Soubrier
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors: Pablo
authors: P
authors: Librado
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.|National High-Throughput DNA Sequencing Center, University of Copenhagen, Øster Farimagsgade 2D, 1353K, Copenhagen, Denmark.
authors: Andaine
authors: A
authors: Seguin-Orlando
authors: Institut Jacques Monod, UMR7592 CNRS, Université Paris 7, 75205, Paris cédex 13, France.
authors: Mélanie
authors: M
authors: Pruvost
authors: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors: Ahmed H
authors: AH
authors: Alfarhan
authors: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors: Saleh A
authors: SA
authors: Alquraishi
authors: Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
authors: Khaled A S
authors: KAS
authors: Al-Rasheid
authors: Palaeogenetics Group, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.|Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland.
authors: Amelie
authors: A
authors: Scheu
authors: Naturwissenschaftliches Referat an der Zentrale, Deutsches Archäologisches Institut, Im Dol 2-6, 14195, Berlin, Germany.
authors: Norbert
authors: N
authors: Beneke
authors: Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany.
authors: Arne
authors: A
authors: Ludwig
authors: Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
authors: Alan
authors: A
authors: Cooper
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.
authors: Eske
authors: E
authors: Willerslev
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark.|Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, 31000, Toulouse, France.
authors: Ludovic
authors: L
authors: Orlando
mesh_terms: D001482:Base Composition; D018899:CpG Islands; D015342:DNA Probes; D000072441:DNA, Ancient / Q000032:analysis*; D059014:High-Throughput Nucleotide Sequencing; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015342:DNA Probes; D000072441:DNA, Ancient
keywords: ancient DNA; capture; enrichment; in-solution