Chloroplast genome‐based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions

The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold‐tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome‐based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole‐genomic DNA using short reads (100–150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo‐based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non‐Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis‐idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast‐based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA. In this study, we assemble 92 whole chloroplast genomes from 12 subalpine plant species (5 conifers and 7 angiosperms) and identify intraspecific variation and lineages that will be useful for evolutionary, phylogeographic and conservation‐focused studies of the threatened subalpine forest biome of Japan and adjacent regions in northeast Asia.