Feb 23, 2012

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

Scientific Reports
María C Avila-ArcosM Thomas P Gilbert

Abstract

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.

Mentioned in this Paper

Zea mays
Ancient DNA
Sequencing
Sequence Determinations, DNA
Plant material (substance)
Clonality (Genetic Analysis)
DNA, Plant
Nested Polymerase Chain Reaction

Related Feeds

Ancient DNA

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, but are notoriously difficult to analyze due to molecular damage and exogenous dna contamination. Discover the latest research on Ancient DNA here.