globalchange  > 过去全球变化的重建
DOI: 10.1371/journal.pone.0089676
论文题名:
Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA
作者: Bastiaan Star; Alexander J. Nederbragt; Marianne H. S. Hansen; Morten Skage; Gregor D. Gilfillan; Ian R. Bradbury; Christophe Pampoulie; Nils Chr Stenseth; Kjetill S. Jakobsen; Sissel Jentoft
刊名: PLOS ONE
ISSN: 1932-6203
出版年: 2014
发表日期: 2014-3-7
卷: 9, 期:3
语种: 英语
英文关键词: Genomic libraries ; Sequence alignment ; Sequence assembly tools ; Ancient DNA ; DNA libraries ; Cod ; Polymerases ; Blunt-end ligation
英文摘要: 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.
URL: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089676&type=printable
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资源类型: 期刊论文
标识符: http://119.78.100.158/handle/2HF3EXSE/19146
Appears in Collections:过去全球变化的重建
影响、适应和脆弱性
科学计划与规划
气候变化与战略
全球变化的国际研究计划
气候减缓与适应
气候变化事实与影响

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作者单位: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Department of Medical Genetics, Oslo University Hospital, Oslo, Norway;Fisheries and Oceans Canada, St. John's, Newfoundland, Canada;Marine Research Institute, Reykjavík, Iceland;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway

Recommended Citation:
Bastiaan Star,Alexander J. Nederbragt,Marianne H. S. Hansen,et al. Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA[J]. PLOS ONE,2014-01-01,9(3)
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