DOI: 10.5281/zenodo.10794021
title: Plant DNA metabarcoding record from a sediment core from Lake Ximen, northeastern Tibetan Plateau

description: 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The raw NGS sequencing data of Lake Ximen have been archived in ENA with the accession code: PRJEB72448.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.

 

 

 

 

 
description: For reanalysis of data, we provide the following data files:

1. OBITools pipeline

a. The raw metabarcoding sequencing data were archived at ENA with the accession code: PRJEB72448.

    Forward: 200629_NB501850_A_L1-4_APMG-14_R1.fastq

    Reverse: 200629_NB501850_A_L1-4_APMG-14_R2.fastq

 

b. Tagfile: associate the sample names in the tagfile which indicate the sample batch number and corresponding controls (DNA extraction blank (BLANK) and PCR negative control (NTC)).

   Filename: Tagfile_XimenCo.txt

 

c. Taxonomy dump files of Eastern Tibetan vascular plant reference libraries

    Filename: Tibet_gh.annotatedDB.zip

 

d. Tibet gh reference databases for taxonomic assignment in OBITools

    Filename: Tibet_gh.fasta

 

e. ObITools script for analyzing the metabarcoding data

    Filename: Obitools_pipeline_XimenCo.txt

 

 

2. Data processing: merging and denoising OBITools data 

a. Output files of OBITools (the Naleng data is attached), used for followed analysis

    Filename: XimenCo_KMD_assigned_uniq_count_clean_l10_c10.fasta.txt

    Filename: NalengCo_KMD_assigned_uniq_count_clean_l10_c10.fasta.txt

 

b. Sample-age file, used for merging and denoising samples.

    Filename: XimenCo-Age.txt

    Filename: NalengCo-Age.txt

 

c. Merge and Denoising script for the output OBItools files.

    Filename: Merge_Denoising.R

 

4. Data processing:  data 

 

d. Output files from Merge and Denoising script

    Filename: XimenCo_id1_samples.csv

 

e. Rarefaction Script

    Filename: Rarefaction.R

 

f. Output files from Rarefaction script

    Filename: XimenCo_rarefied_data.zip