Improving the performance of true single molecule sequencing for ancient DNA.

BMC Genomics
Aurélien GinolhacLudovic Orlando

Abstract

Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existenc...Continue Reading

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Citations

May 12, 2012·BMC Genomics·Mikkel SchubertLudovic Orlando
Dec 10, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Clio Der SarkissianLudovic Orlando
Sep 25, 2015·Molecular Ecology Resources·Cristina GambaLudovic Orlando
Jun 19, 2012·Molecular Phylogenetics and Evolution·Johanna L A PaijmansMichael Hofreiter
Jun 18, 2015·Scientific Reports·Peter B DamgaardMorten E Allentoft
Apr 19, 2013·American Journal of Physical Anthropology·C SosaB Martinez-Jarreta
Mar 13, 2014·Molecular Ecology·C Der SarkissianL Orlando
Mar 30, 2016·Marine Genomics·Isa Schön, Koen Martens
Aug 28, 2015·Genetika·A S DruzhkovaA S Graphodatsky
Jun 10, 2015·Nature Reviews. Genetics·Ludovic OrlandoEske Willerslev
Dec 24, 2014·Journal of Human Evolution·Luca ErminiLudovic Orlando
Aug 28, 2016·Molecular Ecology Resources·Diana I Cruz-DávalosLudovic Orlando
Oct 30, 2016·Molecular Ecology Resources·Sanne BoessenkoolBastiaan Star
Jun 14, 2017·GigaScience·Anna PhilipsMarek Figlerowicz
Mar 28, 2018·Nature Ecology & Evolution·Jessica HendyMatthew J Collins
Apr 10, 2021·Briefings in Bioinformatics·Adrien OlivaYassine Souilmi

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Datasets Mentioned

BETA
SRA045862

Methods Mentioned

BETA
PCR
Illumina sequencing
deamination

Software Mentioned

FigTree
Helicos
R scripts
jModeltest
BLAST
R
blastn
tSMS
PhyML
map Damage package

Related Concepts

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Ancient DNA

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, but are notoriously difficult to analyze due to molecular damage and exogenous dna contamination. Discover the latest research on Ancient DNA here.