Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora

We present a decade-long research initiative of biodiversity genomics, which aimed at sequencing all vascular plant species occurring in the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region. We detail the sampling and sequencing strategies, an online database of genome skimming datasets, and bioinformatic procedures to retrieve sequence data. Based on low coverage shotgun sequencing of 6,105 species, we generated a dataset of 81 orthologous chloroplast loci, including all standard barcodes. Using maximum likelihood, we inferred a species-resolved phylogeny which covers 96% of the flora occurring above treeline in the Alps and 92% of the Arctic Flora, along with many additional non-alpine species to improve species sampling and allow fossil dating. The data released here provide the baseline of a unique, ever-growing genomic resource for various applications such as phylogenomics, systematics, conservation and metabarcoding of the arctic–alpine realm.