Plant sedaDNA metabarcoding from lake core sediments (EN20001) in southwestern Yakutia, Eastern Siberia

The provided dataset includes raw sequencing files from two independent next-generation sequencing (NGS) runs (APMG-39 and APMG-64) conducted on an Illumina platform for samples from Lake Khamra. Sequencing run APMG-39 includes paired-end amplicon sequencing data (forward: 210914_NB501850_A_L1-4_APMG-39_R1.fastq.gz, reverse: 210914_NB501850_A_L1-4_APMG-39_R2.fastq.gz) generated from 23 samples obtained from a lacustrine sediment core (EN20001). Sequencing run APMG-64 includes forward file: 230104_NB501473_A_L1-4_APMG-64_R1.fastq.gz, and a reverse file: 230104_NB501473_A_L1-4_APMG-64_R2.fastq.gz, generated from 26 samples obtained from a lacustrine sediment core (EN20001). Sedimentary ancient DNA (sedaDNA) extraction and PCR setup were conducted in two independent runs (APMG-39 and APMG-64) using samples processed in the dedicated paleogenetic laboratories at the Alfred Wegener Institute (AWI), under a cleaned and UV-irradiated working hood (Biosan, Latvia). DNA extractions (ESM for APMG-39 and EYaL for APMG-64) were performed using the Dneasy PowerSoil Max DNA Isolation Kit (Qiagen, Germany) with about 2.2–6.8 g sediment input, following established protocols (Epp et al. 2019). For PCR we used standard primers targeting the chloroplast trnL P6 loop (Taberlet et al. 2007) amplification of vascular plant DNA metabarcoding. Two pools APMG-39 and APMG-64 of PCR samples were prepared and sent to Fasteris (Genesupport, Fasteris SA, Switzerland) for preparing a PCR-free library (using the metafast protocol) and sequencing in paired-end mode (2x 150 bp) on the NextSeq Illumina sequencing device with NextSeq Mid kit (Illumina). The data from two runs were merged into a single dataset for the final interpretation.