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Library construction for ancient genomics: single strand or double strand? - PubMed

  • ️Wed Jan 01 2014

. 2014 Jun 1;56(6):289-90, 292-6, 298, passim.

doi: 10.2144/000114176. eCollection 2014 Jun.

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Library construction for ancient genomics: single strand or double strand?

E Andrew Bennett et al. Biotechniques. 2014.

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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.

Keywords: DNA library preparation; ancient DNA; next-generation sequencing; palaeogenomics.

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