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...
Published in: | Molecular Ecology Resources |
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2017
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Online Access: | https://curis.ku.dk/portal/da/publications/combining-bleach-and-mild-predigestion-improves-ancient-dna-recovery-from-bones(c52ab951-3951-41d2-a24d-eea3786c652e).html https://doi.org/10.1111/1755-0998.12623 |
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ftcopenhagenunip:oai:pure.atira.dk:publications/c52ab951-3951-41d2-a24d-eea3786c652e 2024-04-28T08:13:02+00:00 Combining bleach and mild predigestion improves ancient DNA recovery from bones Boessenkool, Sanne Hanghøj, Kristian Ebbesen Nistelberger, Heidi M. Der Sarkissian, Clio Gondek, Agata T. Orlando, Ludovic Antoine Alexandre Barrett, James H. Star, Bastiaan 2017-07 https://curis.ku.dk/portal/da/publications/combining-bleach-and-mild-predigestion-improves-ancient-dna-recovery-from-bones(c52ab951-3951-41d2-a24d-eea3786c652e).html https://doi.org/10.1111/1755-0998.12623 eng eng info:eu-repo/semantics/closedAccess Boessenkool , S , Hanghøj , K E , Nistelberger , H M , Der Sarkissian , C , Gondek , A T , Orlando , L A A , Barrett , J H & Star , B 2017 , ' Combining bleach and mild predigestion improves ancient DNA recovery from bones ' , Molecular Ecology Resources , vol. 17 , no. 4 , pp. 742–751 . https://doi.org/10.1111/1755-0998.12623 article 2017 ftcopenhagenunip https://doi.org/10.1111/1755-0998.12623 2024-04-04T17:35:11Z 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 University of Copenhagen: Research Molecular Ecology Resources 17 4 742 751 |
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Open Polar |
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University of Copenhagen: Research |
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ftcopenhagenunip |
language |
English |
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 Ebbesen Nistelberger, Heidi M. Der Sarkissian, Clio Gondek, Agata T. Orlando, Ludovic Antoine Alexandre Barrett, James H. Star, Bastiaan |
spellingShingle |
Boessenkool, Sanne Hanghøj, Kristian Ebbesen Nistelberger, Heidi M. Der Sarkissian, Clio Gondek, Agata T. Orlando, Ludovic Antoine Alexandre Barrett, James H. Star, Bastiaan Combining bleach and mild predigestion improves ancient DNA recovery from bones |
author_facet |
Boessenkool, Sanne Hanghøj, Kristian Ebbesen Nistelberger, Heidi M. Der Sarkissian, Clio Gondek, Agata T. Orlando, Ludovic Antoine Alexandre 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 |
publishDate |
2017 |
url |
https://curis.ku.dk/portal/da/publications/combining-bleach-and-mild-predigestion-improves-ancient-dna-recovery-from-bones(c52ab951-3951-41d2-a24d-eea3786c652e).html https://doi.org/10.1111/1755-0998.12623 |
genre |
atlantic cod |
genre_facet |
atlantic cod |
op_source |
Boessenkool , S , Hanghøj , K E , Nistelberger , H M , Der Sarkissian , C , Gondek , A T , Orlando , L A A , Barrett , J H & Star , B 2017 , ' Combining bleach and mild predigestion improves ancient DNA recovery from bones ' , Molecular Ecology Resources , vol. 17 , no. 4 , pp. 742–751 . https://doi.org/10.1111/1755-0998.12623 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12623 |
container_title |
Molecular Ecology Resources |
container_volume |
17 |
container_issue |
4 |
container_start_page |
742 |
op_container_end_page |
751 |
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1797579692317868032 |