Plant DNA taxa detected in Lake La Thuile sediments (North-western Alps) over the last 6500 years

DOI

This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (4 PCR replicates for plants and 12 for mammals). It has been generated applying the DNA metabarcoding approach on a 5.49-m long sediment cores retrieved by using a UWITEC platform and coring devices. The primers used are g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') (Taberlet, P., et al. Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic acids research, 35(3), e14-e14. (2007)). The sequences were then produced by the Illumina technology (HiSeq instrument). The bioinformatic treatment of the sequences was operated applying the Obitool program (Boyer, F. et al. OBITOOLS:aUNIX-inspired software package for DNAmetabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016)) and following the procedure described in Giguet-Covex et al. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Scientific Reports. 9, 14676 (2019) (DOI https://doi.org/10.1038/s41598-019-50339-1). Further filtering treatments were then applied, as also described in Giguet-Covex et al. 2019. These second treatments allow the removal of 1) taxa assigned to a reference taxon at <95 % of sequence identity, 2) potential contaminations (based on sampling, extraction and PCR controls, and recognition of exotic taxa) and 3) stochastic detections.

Identifier
DOI https://doi.org/10.1594/PANGAEA.958680
Related Identifier https://doi.org/10.1594/PANGAEA.958732
Related Identifier https://doi.org/10.1007/s10113-023-02030-5
Metadata Access https://ws.pangaea.de/oai/provider?verb=GetRecord&metadataPrefix=datacite4&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.958680
Provenance
Creator Giguet-Covex, Charline ORCID logo
Publisher PANGAEA
Publication Year 2023
Funding Reference European Commission https://doi.org/10.13039/501100000780 Crossref Funder ID 655331 https://cordis.europa.eu/project/id/655331 agroPastoral Activities and effects on Landscapes and ErOsion dynAmics in the alps: a new insight from Geological appRoaches and lake sedIment DNA (PALEO-AGRI); Grenoble Alpes University https://doi.org/10.13039/100012952 Crossref Funder ID ANR-15-IDEX-02 CDP Trajectories
Rights Creative Commons Attribution 4.0 International; https://creativecommons.org/licenses/by/4.0/
OpenAccess true
Representation
Language English
Resource Type Dataset
Format text/tab-separated-values
Size 13400 data points
Discipline Earth System Research
Spatial Coverage (6.056 LON, 45.531 LAT); North-western Alps