DOI: 10.5061/dryad.34tmpg4gz
title: Ancient sedimentary plant DNA and pollen dataset from Bolshoe Toko Lake, southeastern Siberia

description: 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.
description: 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 <i>Lycopodium</i> 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.
description: For reanalysis of data we provide the following data
 files: 1. Illumina sequencing raw data of the
 sequencing run: HUA-9. Data files are compressed. HUA-9
 (170927_SND393_A_L006_HUA-9_R1.fastq.gz,
 170927_SND393_A_L006_HUA-9_R2.fastq.gz). 2. Two scripts
 to run the OBITools pipeline with a short description of each
 step. Data analyses with OBITools
 (Script_data_analyses_with_OBITools.txt) Database
 creation with EcoPCR and OBITools
 (Script_Database_creation_for_OBITools.txt) 3. Tagfiles
 needed for the OBITools pipeline with a corresponding file to associate
 the sample names in the tagfiles which indicate the sample batch number
 with the depth and corresponding controls (DNA extraction blank (BLANK)
 and PCR negative control (NTC)). HUA-9:
 HUA-9_tagfile.txt HUA-9_names.txt 4. Taxonomic database
 files needed for the OBITools pipeline (see
 Script_data_analyses_with_OBITools.txt) EMBL database
 (g_h_embl133_final.uniqIDs.fasta) Arctic database
 (arctborbryo_gh.fasta, ecochange.zip) 5. Final data
 tables after bioinformatic analyses with OBITools. For each sequencing run
 we provide two data tables, one with the taxonomic assignment of the EMBL
 and a second with the taxonomic assignment of the Arctic database. Final
 data tables for the pollen analysis. HUA-9
 (HUA9_embl133_final.txt, HUA9_arc_gh_final.txt,
 Bolshoe-Toko_pollen_courtin.xls)