Plant DNA metabarcoding record from a sediment core from Lake Ximen, northeastern Tibetan Plateau

Here, we provide the data processing process for the genetic plant diversity archive from sedimentary ancient DNA (sedaDNA) of Lake Ximen, eastern Tibetan Plateau, China. 

The raw NGS sequencing data of Lake Ximen have been archived in ENA with the accession code: PRJEB72448. the raw NGS sequencing data of Lake Naleng was stored at Zenodo (https://doi.org/10.5061/dryad.vdncjsxth). 

We build a customized East Tibetan reference database for taxonomic classification, consisting of 309 unique sequences (amplicon sequence variants) obtained from 911 specimens representing 890 species (Tibet_gh.fasta).  We collected the species that are naturally distributed at elevations of at least 3,000 m a.s.l. in the TP area and included the corresponding sequences, which were extracted from the P6 loop of trnL (UAA) intron of assembled chloroplast whole genomes. 

Quality filtering, demultiplexing, and taxonomic classification with the Tibet database of the sequencing data were performed via an OBITools pipeline with the script (Obitools_pipeline_XimenCo.txt). The output file (XimenCo_KMD_assigned_uniq_count_clean_l10_c10.fasta.txt) of the OBITools pipeline was further processed with R, using the script (Merge_Denoising.R), do further denoising, sum up PCR replicates and generate a table for rarefaction step. To get effective species richness per sample, We rarefied the data to equal counts for each sample with the script (Rarefaction.R). The output files are used for further statistical analysis.