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

Cristina Gamba; Kristian Ebbesen Hanghøj; Charleen Gaunitz; Ahmed H. Alfarhan; Saleh A. Alquraishi; Khaled A. S. Al-Rasheid; Daniel G. Bradley; Ludovic Antoine Alexandre Orlando

doi:10.1111/1755-0998.12470

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

Cristina Gamba, Kristian Ebbesen Hanghøj, Charleen Gaunitz, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, Daniel G. Bradley, Ludovic Antoine Alexandre Orlando^*

^*Corresponding author for this work

81 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Molecular Ecology Resources
Volume	16
Issue number	2
Pages (from-to)	459-469
Number of pages	11
ISSN	1755-098X
DOIs	https://doi.org/10.1111/1755-0998.12470
Publication status	Published - 1 Mar 2016

Keywords

Ancient DNA
DNA extraction
Palaeogenomics
Ultrashort fragments

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10.1111/1755-0998.12470

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title = "Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing",

abstract = "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.",

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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 - 2016/3/1

Y1 - 2016/3/1

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

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DO - 10.1111/1755-0998.12470

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JO - Molecular Ecology Resources

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

Abstract

Keywords

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