New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

Nathan Wales; Christian Carøe; Marcela Sandoval-Velasco; Cristina Gamba; Ross Barnett; José Alfredo Samaniego; Jazmín Ramos Madrigal; Ludovic Orlando; M. Thomas P. Gilbert

doi:10.2144/000114364

New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

Nathan Wales^*, Christian Carøe, Marcela Sandoval-Velasco, Cristina Gamba, Ross Barnett, José Alfredo Samaniego, Jazmín Ramos Madrigal, Ludovic Orlando, M. Thomas P. Gilbert

^*Corresponding author for this work

Archaeology

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	114364
Pages (from-to)	368-371
Number of pages	4
Journal	Biotechniques
Volume	59
Issue number	6
DOIs	https://doi.org/10.2144/000114364
Publication status	Published - 1 Dec 2015

Keywords

Ancient DNA
DNA library preparation
Next-generation sequencing
Paleogenomics

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10.2144/000114364

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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.",

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AU - Wales, Nathan

AU - Carøe, Christian

AU - Sandoval-Velasco, Marcela

AU - Gamba, Cristina

AU - Barnett, Ross

AU - Samaniego, José Alfredo

AU - Madrigal, Jazmín Ramos

AU - Orlando, Ludovic

AU - Gilbert, M. Thomas P.

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New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

Abstract

Keywords

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