Permafrost-thaw lake development in Central Yakutia: sedimentary ancient DNA and element analyses from a Holocene sediment record

The datasets* are prepared for the manuscripts: Baisheva et al. (2022): "Permafrost-thaw lake development in Central Yakutia – Sedimentary ancient DNA and element analyses from a Holocene sediment record" (submitted) and Glückler et al. (2022): "Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies" (preprint). Also included is the processing of the raw sequencing data using bioinformatics tools.

*The datasets were uploaded into two separate directories containing data and scripts. Each directory contains two main folders APMG_32 (Diatoms) and APMG_33 (Plants). Files of APMG_32 and APMG_33 after downloading have to be merged in the same folder, so the structure of datasets looks like as it is given below:

1)      APMG_32 contains several folders and files of different format:

00.   APMG-32_Metadata - Metadata information including lake geographic coordinates, sample depths and ages, laboratory codes and used primer tag combinations of forward and reverse primers to enable demultiplexing of the sequencing data

FILE:   APMG-32_Metadata.xlsx contains information on sequencing (run number, type, device, mode, forward and reverse tags, read length). Also it includes information on individual samples: name, type, age, depth, extraction number, and PCR number, as well as sediment core name and core section number.

Format: .xlsx

01. Raw_data_APMG-32 – Illumina sequencing raw data.

FILES: 210602_NB501850_A_L1-4_APMG-32_R1.fastq.gz

210602_NB501850_A_L1-4_APMG-32_R2.fastq.gz

Format: Illumina fastq format. The sequence files are compressed as .gz archives. Before using the data with the Obitools script (APMG_32_metabarcoding_rbcL_obi3_Dryad.sh) the datasets need to be uncompressed and converted into .fastq files.

02. Reference_data_rbcl – Database used for taxonomic assignment of diatoms.

FILES:   rbcl_embl143_db.fasta

Obi3_rbcL_database_build.sh - Script for the conversion step.

Format: .fasta and .sh. To use the rbcL database in the Obitools script (APMG_32_metabarcoding_rbcL_obi3_Dryad.sh), the rbcl_embl143_db.fasta needs to be converted to an obi3 database.

03. OBITools_APMG-32 – The metabarcoding pipeline for analyzing the raw sequencing data using OBITools3. 

FILES:   APMG_32_metabarcoding_rbcL_obi3_Dryad.sh - Script to run OBITools3 pipeline with short descriptions and output data.

APMG-32_embl143_rbcL.csv - Output file.

APMG32_tagfile.txt - File contains primer combinations for demultiplexing with Obitools3 (see script: APMG_32_metabarcoding_rbcL_obi3_Dryad.sh).

Format: .csv, .txt and .sh

04. Final_resampled_data_APMG-32:

FILES:   APMG-32_identitylevel0.98_wideformat.csv - Final count data.

APMG-32_final_resampled_scientific_name.csv - Final dataset with filtering threshold of 98%, resampled to the minimal number of counts (n=2050), including diatoms and Nannochloropsis. 

Format: .csv

• • The file APMG-32_final_resampled_data.csv was used for further statistical analyses in Baisheva et al. (2022): "Permafrost-thaw lake development in Central Yakutia – Sedimentary ancient DNA and element analyses from a Holocene sediment record" (submitted). 

2)      APMG_33 contains several folders and files of different format:

00.   APMG-33_Metadata - Contains information on sequencing (run number, type, device, mode, forward and reverse tags, read length). Also it includes information on individual samples: name, type, age, depth, extraction number, and PCR number. As well as sediment core name and core section number.

FILE:   APMG-33_Satagay2_metadata.xlsx

Format: .xlsx 

01.   Raw_data_APMG_33 – Illumina sequencing raw data.

FILES: 210602_NB501850_A_L1-4_APMG-33_R1.fastq.gz

210602_NB501850_A_L1-4_APMG-33_R2.fastq.gz

Format: Illumina fast-q format. The sequence files are compressed as .gz archives. The archives can be uncompressed on linux OS using a gzip -d command.

02. Reference_database_plants – Reference database to run OBITools pipeline with short instruction and script for the conversion step.

FILES:   arctborbryo_gh.fasta

gh_embl143_db_97.fasta

Obi3_arctborbryo_database_build.sh

Obi3_embl_database_build.sh

Format: .fasta and .sh. To use the arctborbryo embl143 database in the Obitools script (APMG-33_obi3_script.sh), .fasta files need to be converted to an obi3 database.

03. OBITools_APMG-33 – The metabarcoding pipeline for analyzing the raw sequencing data using OBITools3. 

FILES:   APMG33_arc_anno.csv - Output file.

APMG33_embl143_anno.csv - Output file.

APMG-33_obi3_script.sh

APMG-33_tagfile.txt

Format: .csv, .txt and .sh. OBITools_APMG-33 has two outputs as taxonomic assignment provided against the EMBL and Arctic databases. 

04. Final_datasets_APMG-33 - EMBL and Arctic assignments were  merged into the one dataset and filtered with 100% threshold. Final datasets separated into macrophytes and terrestrial plants. 

FILES:   APMG-33_identitylevel100_wideformat.csv - Final count data.

APMG-33_macrophytes_resampled_scientific_name.csv - Final dataset of separated macrophytes  and resampled to the minimal number of counts (n=1653). 

APMG-33_terrestrial_families.csv - Final dataset of separated terrestrial plants.

Format: .csv

• The file "APMG-33_macrophytes_resampled_scientific_name.csv" from output data was used for further statistical analyses in Baisheva et al. (2022): "Permafrost-thaw lake development in Central Yakutia – Sedimentary ancient DNA and element analyses from a Holocene sediment record" (submitted). 
• The file "APMG-33_terrestrial_families.csv" of separated terrestrial plants data was used for further statistical analyses in Glückler et al. (2022): "Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies" (preprint).