Plant DNA metabarcoding record from a sediment core from Lake Naleng, southeastern Tibetan Plateau

1. Sedimentary ancient DNA isolation, polymerase chain reactions (PCR), and purification and pooling Sedimentary ancient DNA (sedaDNA) was extracted from about 3–10 g of sediment using the PowerMax® Soil DNA Isolation Kit (MoBio Laboratories, Inc., USA) with a modifed instructions in a dedicated ancient DNA laboratory. The plant sedaDNA was amplified using general plant gh primer targeting the P6 loop (10-143 bp) of chloroplast trnL (Taberlet et al., 2007). Each PCR reaction (25 µL) were prepared in ancient DNA laboratory and amplified in PCR thermocycler in post-PCR laboratory. Then, each PCR batch was run in agarose gel electrophoresis (2%) to check if it can be purified. Each PCR batch was replicated until obtaining two positive PCR products for each sediment sample with associated negative controls. Positive means: the brightest staning is in a range of 100-200 bp and the gene band is evidently longer than one of control. The gene band with length < 50 bp is considered as primer dimer. All qualified PCR replicates were purified with the MinElute PCR Purification Kit (Qiagen, Germany) in post-PCR lab. Afterwards, 1 μL of PCR product was measured with the ds-DNA BR Assay and the Qubit® 2.0 fluorometer (Invitrogen, USA). Finally, all purified PCR products were equimolarly pooled. It should be note that the ancient DNA lab and the post-PCR lab are located in different buildings. The genetic lab work was done in Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Potsdam. 2. High throughput sequencing The pooled PCR products were sequenced on the Illumina HiSeq 2500 platform (2 x 125 bp, paired-end reads) at Fasteris SA sequencing service, Switzerland. The mode is HiSeq High Output Version 4 with the HiSeq SBS Kit v4. Our project resulted in 9.5 Gb with 37,922,797 generated clusters >= Q30. 3. Bioinformatics We used OBITools (Boyer et al., 2016) to do the upstream analysis of the sequencing data. The raw sequecning data (two fastq files), scripts for creating the taxonomic database and analyzing the raw sequencing data are enclosed as well as the tag-sample-matirx.