title: Library construction for ancient genomics: single strand or double strand?
abstract: A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts.
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: E Andrew
authors.initials: EA
authors.lastname: Bennett
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Diyendo
authors.initials: D
authors.lastname: Massilani
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Giulia
authors.initials: G
authors.lastname: Lizzo
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Daligault
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Geigl
authors.affiliation: Institut Jacques Monod, CNRS, Université Paris Diderot, Paris, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Grange
mesh_terms: D000818:Animals; D002417:Cattle; D004247:DNA / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics*; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056665:Mammoths; D010163:Paleontology / Q000379:methods*; D002679:Pan troglodytes; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004277:DNA, Single-Stranded; D004247:DNA
keywords: DNA library preparation; ancient DNA; next-generation sequencing; palaeogenomics