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.
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)
Files
2Scripts.zip
Files
(1.4 GB)
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