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

Citation

Courtin, Jérémy (2021), Ancient sedimentary plant DNA and pollen dataset from Bolshoe Toko Lake, southeastern Siberia, Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4gz

Abstract

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.

Usage Notes

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)