DOI: 10.5061/dryad.k6djh9w4r
title: Plant diversity data from modern sedimentary DNA of lakes in Siberia and China

description: Here we provide a large dataset on genetic plant diversity retrieved from
 surface sedimentary DNA (sedDNA) of lakes from Siberia and China spanning
 over a large environmental gradient. Our dataset encompasses
 sedDNA sequence data of 244 surface lake sediments and 3 soil samples
 originating from Siberia and Chinese lakes. We used a PCR-based
 metabarcoding approach combined with Next-Generation Sequencing to assess
 the modern and local plant diversity in and 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 four independent Illumina sequencing runs
 (ALRK-7, ALRK-3, AGAK-5 and HQD-2).
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 688 PCR products,
 which were sequenced on four independent Illumina sequencing runs (ALRK-7,
 ALRK-3, AGAK-5 and HQD-2). The underlying data set consists of raw
 R1.fastq and R2.fastq files of the four sequencing runs, two scripts that
 explain how to use the OBITools pipeline for data analyses and how to
 prepare taxonomic databases with EcoPCR and OBITools, four different
 tagfiles needed for demultiplexing the sequence raw data into samples,
 three database files for taxonomic assignment and eight final data files,
 two for each sequencing run.
description: For reanalysis of data we provide the following data
 files: 1. Illumina sequencing raw data of four
 sequencing runs (ALRK-7, ALRK-3, AGAK-5, HQD-2). Data files are
 compressed. ALRK-7
 (190820_NB501473_A_L1-4_ALRK-7_R1.fastq.gz,
 190820_NB501473_A_L1-4_ALRK-7_R2.fastq.gz). ALRK-3
 (190128_NB501850_A_L1-4_ALRK-3_R1.fastq.gz,
 190128_NB501850_A_L1-4_ALRK-3_R2.fastq.gz) AGAK-5
 (180912_NB501850_A_L1-4_AGAK-5_R1.fastq.gz,
 180912_NB501850_A_L1-4_AGAK-5_R2.fastq.gz) HQD-2
 (151111_SND104_A_L008_HQD-2_R1.fastq.gz,
 151111_SND104_A_L008_HQD-2_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. Sample name in the
 tagfiles indicates the sequencing run, the sample batch number which
 includes samples and corresponding controls (DNA extraction blank (BLANK)
 and PCR negative control (NTC)). ALRK-7
 (ALRK-7_tagfile.txt) ALRK-3
 (ALRK-3_tagfile.txt) AGAK-5
 (AGAK-5_tagfile.txt) HDQ-2
 (HQD-2_tagfile.txt) 4. Taxonomic database
 files needed for the OBITools pipeline (see
 Script_Database_creation_for_OBITools.txt) 
 EMBL database (g_h_embl138_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. ALRK-7
 (assigned_ALRK-7_unique_clean_embl138_anno.txt,
 assigned_ALRK-7_unique_clean_acrtborbryo_anno.txt)
 ALRK-3 (assigned_ALRK-3_unique_clean_embl138_anno.txt,
 assigned_ALRK-3_unique_clean_acrtborbryo_anno.txt)
 AGAK-5 (assigned_AGAK-5_unique_clean_embl138_anno.txt,
 assigned_AGAK-5_unique_clean_acrtborbryo_anno.txt)
 HQD-2 (assigned_HQD-2_unique_clean_embl138_anno.txt,
 assigned_HQD-2_unique_clean_acrtborbryo_anno.txt)