Fungus and plant sedimentary ancient DNA metabarcoding data from five lakes in Siberia

Here we provide data on lake sediment metabarcoding on sedimentary ancient DNA (sedaDNA) from five lake cores from Siberia. Our dataset includes 70 sediment core samples spanning the last about 47.000 years. We applied a PCR-based approach called metabarcoding to amplify specific DNA target sequences: for fungus metabarcoding, we used the ITS marker alongside with the p6 loop trnL chloroplast marker for vegetation metabarcoding. The amplicons were analysed towards their composition with Next Generation Sequencing on 5 sequencing runs (APMG-17, APMG-20 and ATBH-2 for the fungus data; APMG-12 and APMG-29 for the vegetation). The data were used in the publication of von Hippel et al. (2022, Quaternary Science Reviews, accepted). All samples marked with asterisks in the *samples_ages files were not included in the publication.

Methods
The sedimentary ancient DNA (sedaDNA) was extracted from the samples using the DNeasy PowerMax Soil Kit. We amplified the plant DNA using the established chloroplast p6 trnL loop marker. For the fungus DNA, we used the ITS1 marker by Seeber et al. (2022, Environmental DNA; https://doi.org/10.1002/edn3.315). The plant metabarcoding was conducted in 3 replicates while the fungus metabarcoding was repeated 6 times. In total, we sequenced the data on five different Illumina sequencing runs. Each sequencing data consist of raw R1.fastq and R2.fastq files. We also provide the Obitools pipeline script for the analysis of the data as well as the databases and unique tag-files. The resulting final annotation files are attached as well.