Paging through history: Parchment as a reservoir of ancient DNA for next generation sequencing

TY - JOUR

T1 - Paging through history

T2 - Parchment as a reservoir of ancient DNA for next generation sequencing

AU - Teasdale, M. D.

AU - van Doorn, N. L.

AU - Fiddyment, S.

AU - Webb, C. C.

AU - O’Connor, T.

AU - Hofreiter, M.

AU - Collins, M. J.

AU - Bradley, D. G.

PY - 2015/1/19

Y1 - 2015/1/19

N2 - Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

AB - Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

KW - Ancient DNA

KW - Next generation sequencing

KW - Parchment

KW - Sheep

KW - ZooMS

UR - http://www.scopus.com/inward/record.url?scp=84916239469&partnerID=8YFLogxK

U2 - 10.1098/rstb.2013.0379

DO - 10.1098/rstb.2013.0379

M3 - Journal article

C2 - 25487331

AN - SCOPUS:84916239469

SN - 0962-8436

VL - 370

JO - Philosophical Transactions of the Royal Society B: Biological Sciences

JF - Philosophical Transactions of the Royal Society B: Biological Sciences

IS - 1660

ER -