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 fu

SUBMITTER: Wales N 

PROVIDER: S-EPMC3447772 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature