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.
| Original language | English |
|---|---|
| Article number | e45644 |
| Journal | PLoS ONE |
| Volume | 7 |
| Issue number | 9 |
| Number of pages | 8 |
| ISSN | 1932-6203 |
| DOIs | |
| Publication status | Published - 20 Sept 2012 |
Keywords
- Base Sequence
- Cost-Benefit Analysis
- DNA Primers
- DNA, Plant
- Plants
- Real-Time Polymerase Chain Reaction
- Sequence Analysis, DNA
