Plant diversity data from modern sedimentary DNA of lakes in Siberia and China
Creators
- 1. Alfred Wegener Institute for Polar and Marine Research
- 2. North-Eastern Federal University
- 3. University of Iceland
- 4. Institute of Tibetan Plateau Research
- 5. Capital Normal University
- 6. Zhejiang Normal University
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).
Notes
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)
Files
AGAK5_tagfile.txt
Files
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