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
SN - 1932-6203
VL - 7
JO - PLoS ONE
JF - PLoS ONE
IS - 9
M1 - e45644
ER -
