Metabarcoding plant mock community dataset : Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification bias

This dataset comprises DNA metabarcoding sequences obtained from three mock communities of alpine plants. These communities were designed to investigate quantification and amplification biases in such experiments. The Sper01 primer pair (Taberlet et al., 2007; Taberlet et al., 2018) was used to target the chloroplast trnL (P6 loop) marker. Each mock community was sequenced as a separate Illumina library, resulting in three independent libraries corresponding to three community compositions. High-throughput sequencing was carried out by Fasteris SA (Plan-les-Ouates, Switzerland) on an Illumina NextSeq platform using the Metafast library preparation protocol. The dataset includes sequences from 13 alpine Spermatophyta species. Species (Full name) Short form Amplicon length (bp) GC content (%) Total DNA concentration (ng/µl) Rank (MG) Briza media Bme 53 39.6 183.00 1 Rosa canina Rca 51 31.4 50.80 2 Lotus corniculatus Lco 55 38.2 65.20 3 Populus tremula Ptr 68 25.0 31.40 4 Salvia pratensis Spr 46 26.1 24.40 5 Lonicera xylosteum Lxy 46 32.6 45.80 6 Fraxinus excelsior Fex 39 33.3 22.40 7 Acer campestre Aca 56 39.3 12.20 8 Capsella bursa-pastoris Cbp 48 45.8 38.80 9 Geranium robertianum Gro 53 34.0 15.00 10 Carpinus betulus Cbe 61 27.9 9.14 11 Abies alba Aal 47 44.7 3.58 12 Rhododendron ferrugineum Rfe 46 30.4 3.90 13 Table 1. Plant species included in the three mock communities and their characteristics for the Sper01 marker.Total DNA concentrations were measured by Qubit after extraction. “Rank (MG)” corresponds to decreasing abundance in the MG (geometric) community. Leaf samples were collected in 2021 from the Chartreuse and Belledonne massifs (French Alps), dried in silica gel, and DNA was extracted using the CTAB protocol (Doyle, 1990), except for Carpinus betulus, which was extracted using the DNeasy Plant Mini Kit (Qiagen). Absolute quantification of the Sper01 chloroplast target DNA was obtained using droplet digital PCR (ddPCR; Bio-Rad QX200 system) to account for interspecific variation in chloroplast copy number. For each species, the number of target copies per nanogram of total DNA was estimated. Based on these quantifications, three mock communities were prepared: MU (Uniform community) – equal concentration of target DNA for each species; Forward sequence file: 220930_NB501850_A_L1-4_GWM-1750_R1.fastq.gz Reverse sequence file: 220930_NB501850_A_L1-4_GWM-1750_R2.fastq.gz Demultiplexing metadata file: GWM-1750_U1.ngsfilter MT (Total-DNA community) – equal concentration of total genomic DNA for each species; Forward sequence file: 220930_NB501850_A_L1-4_GWM-1746_R1.fastq.gz Reverse sequence file: 220930_NB501850_A_L1-4_GWM-1746_R2.fastq.gz Demultiplexing metadata file: GWM-1750_U1.ngsfilter MG (Geometric community) – target DNA concentrations following a geometric sequence (1, 1/2, 1/4, ...). Forward sequence file: 220930_NB501850_A_L1-4_GWM-1750_R1.fastq.gz Reverse sequence file: 220930_NB501850_A_L1-4_GWM-1750_R2.fastq.gz Demultiplexing metadata file: GWM-1750_U1.ngsfilter Each community was amplified in 4x20 PCR replicates. Each series of 20 is spiked with a different amount of the following synthetic sequence: accctcagcctcgcccaaggttgaattatgaaacctgtgacggtcgggtc