Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ...
Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to ret...
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Online Access: | https://dx.doi.org/10.5061/dryad.4f4qrfjjc https://datadryad.org/stash/dataset/doi:10.5061/dryad.4f4qrfjjc |
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ftdatacite:10.5061/dryad.4f4qrfjjc 2024-10-13T14:09:45+00:00 Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... Lammers, Youri Taberlet, Pierre Coissac, Eric Elliott, Lucas Dane Merkel, Marie Føreid Pitelkova, Iva PhyloAlps Consortium, Group PhyloNorway Consortium, Group Alsos, Inger Greve 2023 https://dx.doi.org/10.5061/dryad.4f4qrfjjc https://datadryad.org/stash/dataset/doi:10.5061/dryad.4f4qrfjjc en eng Dryad Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 FOS: Biological sciences sedimentary ancient DNA Environmental DNA Multiplexing PCR Phylogeography Dataset dataset 2023 ftdatacite https://doi.org/10.5061/dryad.4f4qrfjjc 2024-10-01T11:13:53Z Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primers could be recovered from the sedaDNA data, where for each sample 28.1 primers containing 34.15 variant sequences ... : DNA was extracted from 20 sediment samples and 4 extraction/sampling negative controls using a modified DNeasy PowerSoil kit (Qiagen, Germany) protocol in the ancient DNA laboratory at TMU. DNA extracts and negative extraction/sampling controls were amplified with a dual-tagged multiplex primer sets that amplified 38 intraspecific regions on the Vaccinium uliginosum chloroplast. The OBITools software package was used for the bioinformatics pipeline. Paired-end reads were aligned using SeqPrep (https://github.com/jstjohn/SeqPrep/releases, v1.2). Merged reads were demultiplexed according to the 4 bp primer tags and identical sequences were collapsed. Singleton sequences and those shorter than 10 bp were removed and putative artifactual sequences were identified and removed from the dataset. The multiplex marker data was identified with a reference dataset. ... Dataset Northern Norway DataCite Norway |
institution |
Open Polar |
collection |
DataCite |
op_collection_id |
ftdatacite |
language |
English |
topic |
FOS: Biological sciences sedimentary ancient DNA Environmental DNA Multiplexing PCR Phylogeography |
spellingShingle |
FOS: Biological sciences sedimentary ancient DNA Environmental DNA Multiplexing PCR Phylogeography Lammers, Youri Taberlet, Pierre Coissac, Eric Elliott, Lucas Dane Merkel, Marie Føreid Pitelkova, Iva PhyloAlps Consortium, Group PhyloNorway Consortium, Group Alsos, Inger Greve Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
topic_facet |
FOS: Biological sciences sedimentary ancient DNA Environmental DNA Multiplexing PCR Phylogeography |
description |
Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primers could be recovered from the sedaDNA data, where for each sample 28.1 primers containing 34.15 variant sequences ... : DNA was extracted from 20 sediment samples and 4 extraction/sampling negative controls using a modified DNeasy PowerSoil kit (Qiagen, Germany) protocol in the ancient DNA laboratory at TMU. DNA extracts and negative extraction/sampling controls were amplified with a dual-tagged multiplex primer sets that amplified 38 intraspecific regions on the Vaccinium uliginosum chloroplast. The OBITools software package was used for the bioinformatics pipeline. Paired-end reads were aligned using SeqPrep (https://github.com/jstjohn/SeqPrep/releases, v1.2). Merged reads were demultiplexed according to the 4 bp primer tags and identical sequences were collapsed. Singleton sequences and those shorter than 10 bp were removed and putative artifactual sequences were identified and removed from the dataset. The multiplex marker data was identified with a reference dataset. ... |
format |
Dataset |
author |
Lammers, Youri Taberlet, Pierre Coissac, Eric Elliott, Lucas Dane Merkel, Marie Føreid Pitelkova, Iva PhyloAlps Consortium, Group PhyloNorway Consortium, Group Alsos, Inger Greve |
author_facet |
Lammers, Youri Taberlet, Pierre Coissac, Eric Elliott, Lucas Dane Merkel, Marie Føreid Pitelkova, Iva PhyloAlps Consortium, Group PhyloNorway Consortium, Group Alsos, Inger Greve |
author_sort |
Lammers, Youri |
title |
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
title_short |
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
title_full |
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
title_fullStr |
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
title_full_unstemmed |
Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA ... |
title_sort |
multiplexing pcr allows the identification of within-species genetic diversity in ancient edna ... |
publisher |
Dryad |
publishDate |
2023 |
url |
https://dx.doi.org/10.5061/dryad.4f4qrfjjc https://datadryad.org/stash/dataset/doi:10.5061/dryad.4f4qrfjjc |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Northern Norway |
genre_facet |
Northern Norway |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.4f4qrfjjc |
_version_ |
1812816813046628352 |