Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA
Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting...
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ftoslouniv:oai:www.duo.uio.no:10852/56795 2023-05-15T15:27:33+02:00 Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel 2014-10-14T15:41:44Z http://hdl.handle.net/10852/56795 http://urn.nb.no/URN:NBN:no-59538 https://doi.org/10.1371/journal.pone.0089676 EN eng Public Library of Science (PLoS) http://urn.nb.no/URN:NBN:no-59538 Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel . Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PLoS ONE. 2014, 9(3) http://hdl.handle.net/10852/56795 1164002 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=9&rft.spage=&rft.date=2014 PLoS ONE 9 3 http://dx.doi.org/10.1371/journal.pone.0089676 URN:NBN:no-59538 Fulltext https://www.duo.uio.no/bitstream/handle/10852/56795/2/journal.pone.0089676.PDF Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ CC-BY 1932-6203 Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2014 ftoslouniv https://doi.org/10.1371/journal.pone.0089676 2020-06-21T08:50:56Z Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5′ and 3′-ends of sequencing reads. The palindromic sequences themselves have specific properties – the bases at the 5′-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3′-end. The terminal 3′ bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3′-end of DNA strands, with the 5′-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias. Article in Journal/Newspaper atlantic cod Gadus morhua Universitet i Oslo: Digitale utgivelser ved UiO (DUO) PLoS ONE 9 3 e89676 |
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Open Polar |
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Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5′ and 3′-ends of sequencing reads. The palindromic sequences themselves have specific properties – the bases at the 5′-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3′-end. The terminal 3′ bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3′-end of DNA strands, with the 5′-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias. |
format |
Article in Journal/Newspaper |
author |
Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel |
spellingShingle |
Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
author_facet |
Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel |
author_sort |
Star, Bastiaan |
title |
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
title_short |
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
title_full |
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
title_fullStr |
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
title_full_unstemmed |
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA |
title_sort |
palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient dna |
publisher |
Public Library of Science (PLoS) |
publishDate |
2014 |
url |
http://hdl.handle.net/10852/56795 http://urn.nb.no/URN:NBN:no-59538 https://doi.org/10.1371/journal.pone.0089676 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_source |
1932-6203 |
op_relation |
http://urn.nb.no/URN:NBN:no-59538 Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel . Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PLoS ONE. 2014, 9(3) http://hdl.handle.net/10852/56795 1164002 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=9&rft.spage=&rft.date=2014 PLoS ONE 9 3 http://dx.doi.org/10.1371/journal.pone.0089676 URN:NBN:no-59538 Fulltext https://www.duo.uio.no/bitstream/handle/10852/56795/2/journal.pone.0089676.PDF |
op_rights |
Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0089676 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
3 |
container_start_page |
e89676 |
_version_ |
1766357981915512832 |