Library construction for ancient genomics: Single strand or double strand?. (June 2014)

• Record Type: Journal Article
• Authors: Bennett, E. Andrew; Massilani, Diyendo; Lizzo, Giulia; Daligault, Julien; Geigl, Eva-Maria; Grange, Thierry
• Is Part Of: Biotechniques. Volume 56:Number 6(2014)
• Page Start: 289
• Page End: 300
• Publication Date: 2014-06
• Subjects: ancient DNA -- palaeogenomics -- DNA library preparation -- next-generation sequencing; Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/000114176
• Languages: English
• ISSNs: 0736-6205

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.