Fungus and plant sedimentary ancient DNA metabarcoding data from five lakes in Siberia

Here we provide data on lake sediment metabarcoding on sedimentary ancient DNA (sedaDNA) from five lake cores from Siberia. Our dataset includes 70 sediment core samples spanning the last about 47.000 years. We applied a PCR-based approach called metabarcoding to amplify specific DNA target sequences: for fungus metabarcoding, we used the ITS marker alongside with the p6 loop trnL chloroplast marker for vegetation metabarcoding. The amplicons were analysed towards their composition with Next Generation Sequencing on 5 sequencing runs (APMG-17, APMG-20 and ATBH-2 for the fungus data; APMG-12 and APMG-29 for the vegetation). The data were used in the publication of von Hippel et al. (2022, Quaternary Science Reviews, accepted). All samples marked with asterisks in the *samples_ages files were not included in the publication. , The sedimentary ancient DNA (sedaDNA) was extracted from the samples using the DNeasy PowerMax Soil Kit. We amplified the plant DNA using the established chloroplast p6 trnL loop marker. For the fungus DNA, we used the ITS1 marker by Seeber et al. (2022, Environmental DNA; https://doi.org/10.1002/edn3.315). The plant metabarcoding was conducted in 3 replicates while the fungus metabarcoding was repeated 6 times. In total, we sequenced the data on five different Illumina sequencing runs. Each sequencing data consist of raw R1.fastq and R2.fastq files. We also provide the Obitools pipeline script for the analysis of the data as well as the databases and unique tag-files. The resulting final annotation files are attached as well., , , # Fungus and plant sedimentary ancient DNA metabarcoding data from five lakes in Siberia Dataset DOI: [10.5061/dryad.05qfttf3x](10.5061/dryad.05qfttf3x) ## Description of the data and file structure This data submission includes ancient DNA metabarcoding results from five Siberian lake sediment cores. It is comprised of fungal and plant DNA datasets (raw data and scripts). The data has been included in the publication von Hippel et al. (2022). [https://doi.org/10.1016/j.quascirev.2022.107758](https://doi.org/10.1016/j.quascirev.2022.107758)Â The dataset is prepared for the manuscript \"Long-term fungus-plant covariation from multi-site sedimentary ancient DNA metabarcoding\". It contains the processing of the raw sequencing data using bioinfomatics tools. We used OBItools (Boyer et al., 2016) and sumaclust (Mercier et al., 2013) for the processing of the sequencing data. In the data files, EB stands for \"extraction blank\" and NTC is \"non-template control\". The age of the samples is ...本数据集提供来自西伯利亚5个湖泊岩芯的沉积古DNA（sedimentary ancient DNA, sedaDNA）湖泊沉积物元条形码（metabarcoding）数据。本数据集包含70个沉积物岩芯样本，时间跨度覆盖近47000年。我们采用基于聚合酶链式反应（polymerase chain reaction, PCR）的元条形码技术扩增特定DNA靶序列：针对真菌元条形码分析，我们使用ITS标记；针对植被元条形码分析，则联用p6环trnL叶绿体标记。扩增子（amplicon）的组成通过下一代测序（Next Generation Sequencing, NGS）进行分析，共开展5轮测序：真菌数据对应APMG-17、APMG-20与ATBH-2测序轮次；植被数据对应APMG-12与APMG-29测序轮次。本数据集已用于von Hippel等人2022年发表于《第四纪科学评论》（Quaternary Science Reviews，已接收）的研究论文。*samples_ages文件中带星号标记的样本未纳入该发表研究。 本研究使用DNeasy PowerMax土壤试剂盒提取样本中的沉积古DNA。我们利用已成熟的叶绿体p6 trnL环标记扩增植物DNA；针对真菌DNA，则采用Seeber等人2022年发表于《环境DNA》（Environmental DNA）的ITS1标记（https://doi.org/10.1002/edn3.315）。植物元条形码实验设置3次生物学重复，真菌元条形码实验则设置6次生物学重复。总体而言，我们依托5轮不同的Illumina测序平台完成数据测序，每轮测序数据均包含原始R1.fastq与R2.fastq文件。此外，本数据集还提供用于数据分析的Obitools流程脚本、数据库文件与唯一标签文件（tag-files），最终的注释文件亦随附于本数据集中。 # 西伯利亚5个湖泊的真菌与植物沉积古DNA元条形码数据集 数据集DOI：10.5061/dryad.05qfttf3x ## 数据与文件结构说明 本提交数据包含来自西伯利亚5个湖泊沉积物岩芯的古DNA元条形码分析结果，涵盖真菌与植物DNA数据集（原始数据与分析脚本）。 本数据集已纳入von Hippel等人2022年发表的研究论文（https://doi.org/10.1016/j.quascirev.2022.107758）。 本数据集为手稿《Long-term fungus-plant covariation from multi-site sedimentary ancient DNA metabarcoding》所制备，包含利用生物信息学工具对原始测序数据的处理流程。本研究使用OBItools（Boyer等人，2016）与sumaclust（Mercier等人，2013）完成测序数据的处理。 在数据文件中，EB代表“提取空白对照”（extraction blank），NTC代表“无模板对照”（non-template control）。样本的年代信息为……