TY - JOUR

T1 - Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

AU - Gamba, Cristina

AU - Hanghøj, Kristian Ebbesen

AU - Gaunitz, Charleen

AU - Alfarhan, Ahmed H.

AU - Alquraishi, Saleh A.

AU - Al-Rasheid, Khaled A. S.

AU - Bradley, Daniel G.

AU - Orlando, Ludovic Antoine Alexandre

PY - 2016

Y1 - 2016

N2 - The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

AB - The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

KW - Ancient DNA

KW - DNA extraction

KW - Palaeogenomics

KW - Ultrashort fragments

U2 - 10.1111/1755-0998.12470

DO - 10.1111/1755-0998.12470

M3 - Journal article

C2 - 26401836

VL - 16

SP - 459

EP - 469

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 2

ER -