Combining bleach and mild predigestion improves ancient DNA recovery from bones.
The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder ai...
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ftunivcam:oai:www.repository.cam.ac.uk:1810/261731 2024-02-04T09:58:47+01:00 Combining bleach and mild predigestion improves ancient DNA recovery from bones. Boessenkool, Sanne Hanghøj, Kristian Nistelberger, Heidi M Der Sarkissian, Clio Gondek, Agata T Orlando, Ludovic Barrett, James H Star, Bastiaan 2017-07 Print-Electronic application/pdf https://www.repository.cam.ac.uk/handle/1810/261731 https://doi.org/10.17863/CAM.6941 eng eng Wiley http://dx.doi.org/10.1111/1755-0998.12623 Mol Ecol Resour https://www.repository.cam.ac.uk/handle/1810/261731 doi:10.17863/CAM.6941 Atlantic cod DNA extraction ancient DNA contamination high-throughput sequencing horse Animals Bone and Bones DNA Ancient Gadus morhua Gene Library High-Throughput Nucleotide Sequencing Horses Sequence Analysis Sodium Hypochlorite Article 2017 ftunivcam https://doi.org/10.17863/CAM.6941 2024-01-11T23:24:23Z The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing. Article in Journal/Newspaper atlantic cod Gadus morhua Apollo - University of Cambridge Repository |
institution |
Open Polar |
collection |
Apollo - University of Cambridge Repository |
op_collection_id |
ftunivcam |
language |
English |
topic |
Atlantic cod DNA extraction ancient DNA contamination high-throughput sequencing horse Animals Bone and Bones DNA Ancient Gadus morhua Gene Library High-Throughput Nucleotide Sequencing Horses Sequence Analysis Sodium Hypochlorite |
spellingShingle |
Atlantic cod DNA extraction ancient DNA contamination high-throughput sequencing horse Animals Bone and Bones DNA Ancient Gadus morhua Gene Library High-Throughput Nucleotide Sequencing Horses Sequence Analysis Sodium Hypochlorite Boessenkool, Sanne Hanghøj, Kristian Nistelberger, Heidi M Der Sarkissian, Clio Gondek, Agata T Orlando, Ludovic Barrett, James H Star, Bastiaan Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
topic_facet |
Atlantic cod DNA extraction ancient DNA contamination high-throughput sequencing horse Animals Bone and Bones DNA Ancient Gadus morhua Gene Library High-Throughput Nucleotide Sequencing Horses Sequence Analysis Sodium Hypochlorite |
description |
The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing. |
format |
Article in Journal/Newspaper |
author |
Boessenkool, Sanne Hanghøj, Kristian Nistelberger, Heidi M Der Sarkissian, Clio Gondek, Agata T Orlando, Ludovic Barrett, James H Star, Bastiaan |
author_facet |
Boessenkool, Sanne Hanghøj, Kristian Nistelberger, Heidi M Der Sarkissian, Clio Gondek, Agata T Orlando, Ludovic Barrett, James H Star, Bastiaan |
author_sort |
Boessenkool, Sanne |
title |
Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
title_short |
Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
title_full |
Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
title_fullStr |
Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
title_full_unstemmed |
Combining bleach and mild predigestion improves ancient DNA recovery from bones. |
title_sort |
combining bleach and mild predigestion improves ancient dna recovery from bones. |
publisher |
Wiley |
publishDate |
2017 |
url |
https://www.repository.cam.ac.uk/handle/1810/261731 https://doi.org/10.17863/CAM.6941 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_relation |
https://www.repository.cam.ac.uk/handle/1810/261731 doi:10.17863/CAM.6941 |
op_doi |
https://doi.org/10.17863/CAM.6941 |
_version_ |
1789963349020114944 |