TY - JOUR
T1 - Experimental conditions improving in-solution target enrichment for ancient DNA
AU - Cruz-Dávalos, Diana I.
AU - Llamas, Bastien
AU - Gaunitz, Charleen
AU - Fages, Antoine Alphonse
AU - Gamba, Cristina
AU - Soubrier, Julien
AU - Sanz, Pablo Librado
AU - Seguin-Orlando, Andaine
AU - Pruvost, Mélanie
AU - Alfarhan, Ahmed H.
AU - Alquraishi, Saleh A.
AU - Al-Rasheid, Khaled A. S.
AU - Scheu, Amelie
AU - Beneke, Norbert
AU - Ludwig, Arne
AU - Cooper, Alan
AU - Willerslev, Eske
AU - Orlando, Ludovic Antoine Alexandre
N1 - © 2016 John Wiley & Sons Ltd.
PY - 2017/5
Y1 - 2017/5
N2 - 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.
AB - 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.
U2 - 10.1111/1755-0998.12595
DO - 10.1111/1755-0998.12595
M3 - Journal article
C2 - 27566552
VL - 17
SP - 508
EP - 522
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 3
ER -