True single-molecule DNA sequencing of a pleistocene horse bone

Research output: Contribution to journalJournal articleResearchpeer-review

Standard

True single-molecule DNA sequencing of a pleistocene horse bone. / Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Raghavan, Maanasa; Mouatt, Julia Thidamarth Vilstrup; Rasmussen, Morten; Magnussen, Kim; Steinmann, Kathleen E.; Kapranov, Philipp; Thompson, John F.; Zazula, Grant; Froese, Duane; Moltke, Ida; Shapiro, Beth; Hofreiter, Michael; Al-Rasheid, Khaled A. S.; Gilbert, M. Thomas P.; Willerslev, Eske.

In: Genome Research, Vol. 21, No. 10, 2011, p. 1705-1719.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Orlando, LAA, Ginolhac, A, Raghavan, M, Mouatt, JTV, Rasmussen, M, Magnussen, K, Steinmann, KE, Kapranov, P, Thompson, JF, Zazula, G, Froese, D, Moltke, I, Shapiro, B, Hofreiter, M, Al-Rasheid, KAS, Gilbert, MTP & Willerslev, E 2011, 'True single-molecule DNA sequencing of a pleistocene horse bone', Genome Research, vol. 21, no. 10, pp. 1705-1719. https://doi.org/10.1101/gr.122747.111

APA

Orlando, L. A. A., Ginolhac, A., Raghavan, M., Mouatt, J. T. V., Rasmussen, M., Magnussen, K., ... Willerslev, E. (2011). True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research, 21(10), 1705-1719. https://doi.org/10.1101/gr.122747.111

Vancouver

Orlando LAA, Ginolhac A, Raghavan M, Mouatt JTV, Rasmussen M, Magnussen K et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research. 2011;21(10):1705-1719. https://doi.org/10.1101/gr.122747.111

Author

Orlando, Ludovic Antoine Alexandre ; Ginolhac, Aurélien ; Raghavan, Maanasa ; Mouatt, Julia Thidamarth Vilstrup ; Rasmussen, Morten ; Magnussen, Kim ; Steinmann, Kathleen E. ; Kapranov, Philipp ; Thompson, John F. ; Zazula, Grant ; Froese, Duane ; Moltke, Ida ; Shapiro, Beth ; Hofreiter, Michael ; Al-Rasheid, Khaled A. S. ; Gilbert, M. Thomas P. ; Willerslev, Eske. / True single-molecule DNA sequencing of a pleistocene horse bone. In: Genome Research. 2011 ; Vol. 21, No. 10. pp. 1705-1719.

Bibtex

@article{5cb6768183744e0688d6fa7828db0262,
title = "True single-molecule DNA sequencing of a pleistocene horse bone",
abstract = "Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first {"}true single molecule sequencing{"} of ancient DNA. We generated 115.9Mb and 76.9Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules as required for second-generation sequencing introduce biases into the data, that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third- generation sequencing approaches.",
author = "Orlando, {Ludovic Antoine Alexandre} and Aur{\'e}lien Ginolhac and Maanasa Raghavan and Mouatt, {Julia Thidamarth Vilstrup} and Morten Rasmussen and Kim Magnussen and Steinmann, {Kathleen E.} and Philipp Kapranov and Thompson, {John F.} and Grant Zazula and Duane Froese and Ida Moltke and Beth Shapiro and Michael Hofreiter and Al-Rasheid, {Khaled A. S.} and Gilbert, {M. Thomas P.} and Eske Willerslev",
year = "2011",
doi = "10.1101/gr.122747.111",
language = "English",
volume = "21",
pages = "1705--1719",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "10",

}

RIS

TY - JOUR

T1 - True single-molecule DNA sequencing of a pleistocene horse bone

AU - Orlando, Ludovic Antoine Alexandre

AU - Ginolhac, Aurélien

AU - Raghavan, Maanasa

AU - Mouatt, Julia Thidamarth Vilstrup

AU - Rasmussen, Morten

AU - Magnussen, Kim

AU - Steinmann, Kathleen E.

AU - Kapranov, Philipp

AU - Thompson, John F.

AU - Zazula, Grant

AU - Froese, Duane

AU - Moltke, Ida

AU - Shapiro, Beth

AU - Hofreiter, Michael

AU - Al-Rasheid, Khaled A. S.

AU - Gilbert, M. Thomas P.

AU - Willerslev, Eske

PY - 2011

Y1 - 2011

N2 - Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9Mb and 76.9Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules as required for second-generation sequencing introduce biases into the data, that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third- generation sequencing approaches.

AB - Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9Mb and 76.9Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules as required for second-generation sequencing introduce biases into the data, that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third- generation sequencing approaches.

U2 - 10.1101/gr.122747.111

DO - 10.1101/gr.122747.111

M3 - Journal article

VL - 21

SP - 1705

EP - 1719

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 10

ER -

ID: 33910458