Ancient sedimentary plant DNA and pollen dataset from Bolshoe Toko Lake, southeastern Siberia

Here we provide a dataset on genetic and pollen plant diversity retrieved from sedimentary ancient DNA (sedaDNA) of the Bolshoe Toko lake from southeastern Siberia. Our dataset encompasses sedaDNA sequence data of 54 lake sediment samples and pollen grain counts of 67 lake sediments samples. We used a PCR-based metabarcoding approach combined with Next-Generation Sequencing to assess the past, local plant diversity around the analysed lake localities. As a plant specific metabarcode we applied the established chloroplastidal P6 loop trnL marker for plant diversity assessment. PCR products were sequenced on one Illumina sequencing run (HUA-9). Pollen and non-pollen palynomorphs (NPP) were identified using a light microscope using pollen atlases and pollen reference collections at the Arctic and Antarctic Research Institute (Sankt-Petersburg) and the Alfred Wegener Institute.

Methods
We extracted sedimentary DNA from lake surface samples by using the DNeasy PowerMax Soil Kit and PowerMax Soil DNA Isolation kit. Further, we used a PCR-based metabarcoding approach combined with Next-Generation Sequencing. As a plant specific metabarcode we applied the established chloroplastidal P6 loop trnL marker for plant diversity assessment and amplified plant DNA from sedimentary DNA extracts. Resulting PCR products were replicated for each sample, resulting in a total of 125 PCR products, which were sequenced on one Illumina sequencing run (HUA-9). The underlying data set consists of raw R1.fastq and R2.fastq files of the sequencing run, two scripts that explain how to use the OBITools pipeline for data analyses and how to prepare taxonomic databases with EcoPCR and OBITools, the tagfile needed for demultiplexing the sequence raw data into samples, three database files for taxonomic assignment and two final data files.

For each sample, 3 g (wet weight) were taken for sample preparation. Standard preparation including KOH, HCl treatment, boiling with HF, and acetolysis was used to concentrate palynomorphs. A Lycopodium spore tablet (batch no. 1031; n = 20,848±1460) was added to each sample to allow to calculate pollen concentration. Palynomorphs were identified using a light microscope (Zeiss Axioskop 2) under 400–600× magnification. At least 300 terrestrial plant pollen grains were counted in each sample. Pollen atlases and pollen reference collections at the Arctic and Antarctic Research Institute (Sankt-Petersburg) and the Alfred Wegener Institute were used for taxonomic identification of pollen and spores. The underlying data set consist on 1 final data file with pollen concentration and pollen counts for each samples.