title: New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.
abstract: An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained <3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.|Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Christian
authors.initials: C
authors.lastname: Carøe
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Marcela
authors.initials: M
authors.lastname: Sandoval-Velasco
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gamba
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Ross
authors.initials: R
authors.lastname: Barnett
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: José Alfredo
authors.initials: JA
authors.lastname: Samaniego
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Jazmín Ramos
authors.initials: JR
authors.lastname: Madrigal
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.|Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
mesh_terms: D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D015723:Gene Library; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000639:trends
chemical_list: D004277:DNA, Single-Stranded; D004247:DNA
keywords: DNA library preparation; ancient DNA; next-generation sequencing; paleogenomics