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

被引：51

作者：

Bennett, E. Andrew ^{[1
]}

Massilani, Diyendo ^{[1
]}

Lizzo, Giulia ^{[1
]}

Daligault, Julien ^{[1
]}

Geigl, Eva-Maria ^{[1
]}

Grange, Thierry ^{[1
]}

机构：

[1] Univ Paris Diderot, Inst Jacques Monod, CNRS, Paris, France

来源：

BIOTECHNIQUES | 2014年 / 56卷 / 06期

关键词：

ancient DNA; palaeogenomics; DNA library preparation; next-generation sequencing; DNA-SEQUENCES; NEANDERTHAL;

D O I：

10.2144/000114176

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：289 / +

页数：9

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