title: Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA.
abstract: The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
authors.forename: María C
authors.initials: MC
authors.lastname: Avila-Arcos
authors.forename: Enrico
authors.initials: E
authors.lastname: Cappellini
authors.forename: J Alberto
authors.initials: JA
authors.lastname: Romero-Navarro
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
authors.forename: J Víctor
authors.initials: JV
authors.lastname: Moreno-Mayar
authors.forename: Morten
authors.initials: M
authors.lastname: Rasmussen
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Fordyce
authors.forename: Rafael
authors.initials: R
authors.lastname: Montiel
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vielle-Calzada
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
mesh_terms: D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification*; D010944:Plants / Q000235:genetics; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant