Plant DNA taxa detected in Lake Anterne sediments (North-western Alps) over the Holocene


This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (2 sample replicates, 2 extraction replicates by sample and 2 polymerase chain reaction (PCR) replicates by extractions, so 8 replicates in total). It has been generated applying the DNA metabarcoding approach on a 20-m long sediment cores retrieved by using a uwitec gravity corer and a NIEDERREITER piston corer. 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 DNA metabarcoding. 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 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.

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Metadata Access
Creator Giguet-Covex, Charline ORCID logo
Publisher PANGAEA
Publication Year 2024
Funding Reference European Commission Crossref Funder 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 Crossref Funder ID ANR-15-IDEX-02 CDP Trajectories
Rights Creative Commons Attribution 4.0 International; Data access is restricted (moratorium, sensitive data, license constraints);
OpenAccess false
Resource Type Dataset
Format text/tab-separated-values
Size 37200 data points
Discipline Earth System Research
Spatial Coverage (6.798 LON, 45.991 LAT)
Temporal Coverage Begin 2007-09-05T00:00:00Z
Temporal Coverage End 2007-09-15T00:00:00Z