Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA
Boessenkool_Blocker_seqBoessenkool_Blocker_seq_id Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause fa...
Main Authors: | , , , , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
Data Archiving and Networked Services (DANS)
2020
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.t33v4k14 |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::48bb1ac8373daca5e889e66f56803bea |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::48bb1ac8373daca5e889e66f56803bea 2023-05-15T17:57:13+02:00 Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA Boessenkool, Sanne Epp, Laura S. Haile, James Bellemain, Eva Edwards, Mary Coissac, Eric Willerslev, Eske Brochmann, Christian 2020-06-25 https://doi.org/10.5061/dryad.t33v4k14 undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.t33v4k14 https://dx.doi.org/10.5061/dryad.t33v4k14 lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:81375 10.5061/dryad.t33v4k14 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81375 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Life sciences medicine and health care DNA Barcoding Genomics/Proteomics Mammalia Bioinfomatics/Phyloinfomatics Mammals envir archeo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.t33v4k14 2023-01-22T16:52:07Z Boessenkool_Blocker_seqBoessenkool_Blocker_seq_id Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we first optimised the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (C. antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analysis, the PCR can be biased towards amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified. Dataset permafrost Siberia Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care DNA Barcoding Genomics/Proteomics Mammalia Bioinfomatics/Phyloinfomatics Mammals envir archeo |
spellingShingle |
Life sciences medicine and health care DNA Barcoding Genomics/Proteomics Mammalia Bioinfomatics/Phyloinfomatics Mammals envir archeo Boessenkool, Sanne Epp, Laura S. Haile, James Bellemain, Eva Edwards, Mary Coissac, Eric Willerslev, Eske Brochmann, Christian Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
topic_facet |
Life sciences medicine and health care DNA Barcoding Genomics/Proteomics Mammalia Bioinfomatics/Phyloinfomatics Mammals envir archeo |
description |
Boessenkool_Blocker_seqBoessenkool_Blocker_seq_id Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we first optimised the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (C. antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analysis, the PCR can be biased towards amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified. |
format |
Dataset |
author |
Boessenkool, Sanne Epp, Laura S. Haile, James Bellemain, Eva Edwards, Mary Coissac, Eric Willerslev, Eske Brochmann, Christian |
author_facet |
Boessenkool, Sanne Epp, Laura S. Haile, James Bellemain, Eva Edwards, Mary Coissac, Eric Willerslev, Eske Brochmann, Christian |
author_sort |
Boessenkool, Sanne |
title |
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
title_short |
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
title_full |
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
title_fullStr |
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
title_full_unstemmed |
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA |
title_sort |
data from: blocking human contaminant dna during pcr allows amplification of rare mammal species from sedimentary ancient dna |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.t33v4k14 |
genre |
permafrost Siberia |
genre_facet |
permafrost Siberia |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:81375 10.5061/dryad.t33v4k14 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:81375 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.t33v4k14 https://dx.doi.org/10.5061/dryad.t33v4k14 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.t33v4k14 |
_version_ |
1766165598095540224 |