Single‐tube library preparation for degraded DNA
Abstract In recent years, massive parallel sequencing has revolutionised the study of degraded DNA , thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipula...
Published in: | Methods in Ecology and Evolution |
---|---|
Main Authors: | , , , , , , , , |
Other Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2017
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1111/2041-210x.12871 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F2041-210X.12871 https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/2041-210X.12871 https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 |
id |
crwiley:10.1111/2041-210x.12871 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1111/2041-210x.12871 2024-06-23T07:51:58+00:00 Single‐tube library preparation for degraded DNA Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel Holger S. Samaniego, José A. Wales, Nathan Sicheritz‐Pontén, Thomas Gilbert, M. Thomas P. Johnston, Susan DeGregorio Family Foundation H2020 European Research Council Danmarks Grundforskningsfond 2017 http://dx.doi.org/10.1111/2041-210x.12871 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F2041-210X.12871 https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/2041-210X.12871 https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Methods in Ecology and Evolution volume 9, issue 2, page 410-419 ISSN 2041-210X 2041-210X journal-article 2017 crwiley https://doi.org/10.1111/2041-210x.12871 2024-06-11T04:46:09Z Abstract In recent years, massive parallel sequencing has revolutionised the study of degraded DNA , thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA . In this study, we compare four Illumina library preparation protocols, including two “single‐tube” methods developed for this study with the explicit aim of improving data quality and reducing preparation time and expenses. The methods are tested on grey wolf ( Canis lupus ) museum specimens. We found single‐tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%. Given the advantages of single‐tube library preparations, we anticipate these methods will be of considerable interest to the growing field of paleogenomics and other applications investigating degraded DNA . Article in Journal/Newspaper Canis lupus Wiley Online Library Methods in Ecology and Evolution 9 2 410 419 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
Abstract In recent years, massive parallel sequencing has revolutionised the study of degraded DNA , thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA . In this study, we compare four Illumina library preparation protocols, including two “single‐tube” methods developed for this study with the explicit aim of improving data quality and reducing preparation time and expenses. The methods are tested on grey wolf ( Canis lupus ) museum specimens. We found single‐tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%. Given the advantages of single‐tube library preparations, we anticipate these methods will be of considerable interest to the growing field of paleogenomics and other applications investigating degraded DNA . |
author2 |
Johnston, Susan DeGregorio Family Foundation H2020 European Research Council Danmarks Grundforskningsfond |
format |
Article in Journal/Newspaper |
author |
Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel Holger S. Samaniego, José A. Wales, Nathan Sicheritz‐Pontén, Thomas Gilbert, M. Thomas P. |
spellingShingle |
Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel Holger S. Samaniego, José A. Wales, Nathan Sicheritz‐Pontén, Thomas Gilbert, M. Thomas P. Single‐tube library preparation for degraded DNA |
author_facet |
Carøe, Christian Gopalakrishnan, Shyam Vinner, Lasse Mak, Sarah S. T. Sinding, Mikkel Holger S. Samaniego, José A. Wales, Nathan Sicheritz‐Pontén, Thomas Gilbert, M. Thomas P. |
author_sort |
Carøe, Christian |
title |
Single‐tube library preparation for degraded DNA |
title_short |
Single‐tube library preparation for degraded DNA |
title_full |
Single‐tube library preparation for degraded DNA |
title_fullStr |
Single‐tube library preparation for degraded DNA |
title_full_unstemmed |
Single‐tube library preparation for degraded DNA |
title_sort |
single‐tube library preparation for degraded dna |
publisher |
Wiley |
publishDate |
2017 |
url |
http://dx.doi.org/10.1111/2041-210x.12871 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F2041-210X.12871 https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/2041-210X.12871 https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12871 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Methods in Ecology and Evolution volume 9, issue 2, page 410-419 ISSN 2041-210X 2041-210X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/2041-210x.12871 |
container_title |
Methods in Ecology and Evolution |
container_volume |
9 |
container_issue |
2 |
container_start_page |
410 |
op_container_end_page |
419 |
_version_ |
1802643139781984256 |