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Diatom sedimentary ancient DNA metabarcoding from western Fram Strait and Kronotsky Peninsula

Citation

Zimmermann, Heike et al. (2020), Diatom sedimentary ancient DNA metabarcoding from western Fram Strait and Kronotsky Peninsula, Dryad, Dataset, https://doi.org/10.5061/dryad.bnzs7h481

Abstract

In this study we use sedimentary ancient DNA metabarcoding from two marine sediment cores. The first Kastenlot core MSM05/5-712-2 was taken at western Fram Strait (subarctic North Atlantic) from which we collected 12 samples including one biological replicate. The second Kastenlot core SO201-2-12KL was retrieved from Kamchatka Strait (subarctic North Pacific) from which we collected 9 samples and 2 samples were collected from a pilot core taken next to the Kastenlot core. Total DNA was extracted from approximately 2ml sediment per sample in 3 batches with up to 9 samples and one extraction blank. Total DNA was concentrated and if necessary diluted to 2.5 ng/µl. For each batch we performed PCRs in triplicates including a PCR no template control (NTC). We amplified a diatom-specific, 76 bp long part of the rbcL gene with tagged primers Diat_rbcL_705F (AACAGGTGAAGTTAAAGGTTCATAYTT) and Diat_rbcL_808R (TGTAACCCATAACTAAATCGATCAT). The PCR-products were purified and pooled in equal concentrations. The sequencing library was prepared with the Mid Output kit v. 2 according to the Fasteris Metafast protocol for low complexity amplicon sequencing and checked by qPCR. The library was sequenced (2 x 150 bp, paired-end) on the Illumina NextSeq 500 at the Fasteris SA sequencing service (Switzerland). For two samples we sequenced 4 PCR-products and for two samples we could only get 2 PCR-products with sufficient DNA content for sequencing.

Methods

Here, we provide the raw paired-end sequencing data received from Fasteris as gz-compressed fastq files (frorward reads: 190128_NB501850_A_L1-4_AGAK-6_R1.fastq.gz; reverse reads: 190128_NB501850_A_L1-4_AGAK-6_R2.fastq.gz). Data processing, which includes assignment of the sequencing reads to the different samples with a tagfile (tagfile_AGAK-6.txt), denoising and taxonomic assignment of reads, was performed with the OBITools pipeline (https://pythonhosted.org/OBITools/welcome.html). The script containing the commands used to process the data is provided (AGAK-6.log). Taxonomic assignment based on (diat_embl138_final.fasta). Finally, we provide the resulting table which was annotated with the age and depth information per sample (AGAK-6_rbcL_embl138.txt).

 

Funding

European Research Council