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 for genome skimming datasets, and bioinformatic procedures to retrieve sequence data. Based on low coverage shotgun sequencing of 6,105 vascular plant species, we generated a dataset of 81 orthologous chloroplast loci, including all standard barcodes. We inferred a species-resolved phylogeny, which includes many additional non-alpine in-groups and out-groups to improve species sampling and allow fossil dating, and thus constitutes a reference phylogenetic dataset about the flora of the Alps and the Arctic. The data released here provide the baseline to develop a unique, ever-growing genomic resource for various research applications such as phylogenomics, systematics, conservation and metabarcoding of the arctic-alpine realm.