Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Choosing the best plant for the job : a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing. / Wales, Nathan; Romero-Navarro, J. Alberto; Cappellini, Enrico; Gilbert, Tom.

In: PLoS ONE, Vol. 7, No. 9, e45644, 20.09.2012.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Wales, N, Romero-Navarro, JA, Cappellini, E & Gilbert, T 2012, 'Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing', PLoS ONE, vol. 7, no. 9, e45644. https://doi.org/10.1371/journal.pone.0045644

APA

Wales, N., Romero-Navarro, J. A., Cappellini, E., & Gilbert, T. (2012). Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing. PLoS ONE, 7(9), [e45644]. https://doi.org/10.1371/journal.pone.0045644

Vancouver

Wales N, Romero-Navarro JA, Cappellini E, Gilbert T. Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing. PLoS ONE. 2012 Sep 20;7(9). e45644. https://doi.org/10.1371/journal.pone.0045644

Author

Wales, Nathan ; Romero-Navarro, J. Alberto ; Cappellini, Enrico ; Gilbert, Tom. / Choosing the best plant for the job : a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing. In: PLoS ONE. 2012 ; Vol. 7, No. 9.

Bibtex

@article{8c3f6af75a834715bebb0efc0b9447e3,
title = "Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing",
abstract = "DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.",
keywords = "Base Sequence, Cost-Benefit Analysis, DNA Primers, DNA, Plant, Plants, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA",
author = "Nathan Wales and Romero-Navarro, {J. Alberto} and Enrico Cappellini and Tom Gilbert",
year = "2012",
month = sep,
day = "20",
doi = "10.1371/journal.pone.0045644",
language = "English",
volume = "7",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

RIS

TY - JOUR

T1 - Choosing the best plant for the job

T2 - a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing

AU - Wales, Nathan

AU - Romero-Navarro, J. Alberto

AU - Cappellini, Enrico

AU - Gilbert, Tom

PY - 2012/9/20

Y1 - 2012/9/20

N2 - DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.

AB - DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant) and exogenous (derived from other sources) DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.

KW - Base Sequence

KW - Cost-Benefit Analysis

KW - DNA Primers

KW - DNA, Plant

KW - Plants

KW - Real-Time Polymerase Chain Reaction

KW - Sequence Analysis, DNA

U2 - 10.1371/journal.pone.0045644

DO - 10.1371/journal.pone.0045644

M3 - Journal article

C2 - 23029156

VL - 7

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 9

M1 - e45644

ER -

ID: 48848019