Plant DNA taxa detected in Lake Gers sediments (North-western Alps) over the last 4600 years


This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (8 PCR replicates). It has been produced by applying the DNA metabarcoding approach on a 5.8-m long sediment cores retrieved by using an uwitec 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 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 Then, other filtering processing were performed as also described in Giguet-Covex et al. 2019. This second treatment 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.

Related Identifier IsPartOf
Related Identifier References
Metadata Access
Creator Giguet-Covex, Charline ORCID logo; Ficetola, Francesco Gentile; Bajard, Manon 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 17219 data points
Discipline Earth System Research
Spatial Coverage (6.730 LON, 46.027 LAT); North-western Alps