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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946424/ https://www.ncbi.nlm.nih.gov/pubmed/24608104 http://dx.doi.org/10.1371/journal.pone.0089676 |
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author | Star, Bastiaan Nederbragt, Alexander J. Hansen, Marianne H. S. Skage, Morten Gilfillan, Gregor D. Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Chr Jakobsen, Kjetill S. Jentoft, Sissel |
author_facet | Star, Bastiaan Nederbragt, Alexander J. Hansen, Marianne H. S. Skage, Morten Gilfillan, Gregor D. Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Chr Jakobsen, Kjetill S. Jentoft, Sissel |
author_sort | Star, Bastiaan |
collection | PubMed |
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 | Online Article Text |
id | pubmed-3946424 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39464242014-03-10 Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA Star, Bastiaan Nederbragt, Alexander J. Hansen, Marianne H. S. Skage, Morten Gilfillan, Gregor D. Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Chr Jakobsen, Kjetill S. Jentoft, Sissel PLoS One Research Article 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. Public Library of Science 2014-03-07 /pmc/articles/PMC3946424/ /pubmed/24608104 http://dx.doi.org/10.1371/journal.pone.0089676 Text en © 2014 Star et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Star, Bastiaan Nederbragt, Alexander J. Hansen, Marianne H. S. Skage, Morten Gilfillan, Gregor D. Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Chr Jakobsen, Kjetill S. Jentoft, Sissel Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946424/ https://www.ncbi.nlm.nih.gov/pubmed/24608104 http://dx.doi.org/10.1371/journal.pone.0089676 |
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