Complete chloroplast genome sequences of two miniaturized <i>Galium</i> species (Rubiaceae) from Yakushima Island, Japan

Yakushima Island is a hotspot of plant biodiversity in the Japanese Archipelago. Over 80 herbaceous species on the island have evolved into miniaturized forms because of grazing pressure from native deer. We focused on two miniaturized taxa, Galium kamtschaticum var. minus and G. pogonanthum var. yakumontanum (Rubiaceae), which are endemic to the island. Despite their evolutionary and conservation importance, genetic resources for these threatened taxa are limited. Therefore, we aimed to generate complete chloroplast genome sequences for these taxa as a first step toward future research. Using a genome-skimming method, we constructed circular chloroplast genomes of 154,980 and 153,867 bp for G. kamtschaticum var. minus and G. pogonanthum var. yakumontanum, respectively. Both genomes exhibited a typical quadripartite structure and largely conserved organization, with differences mainly restricted to the inverted repeat (IR) boundaries. They contained 135 and 134 genes, respectively, and the difference in the total gene number was explained by the effect of IR boundary placement on the copy number of rps19. We detected 302 single-nucleotide polymorphisms across the two chloroplast genomes, providing candidates for the development of diagnostic markers. Phylogenetic analysis of the complete chloroplast genome sequences of Rubiaceae species revealed that the two Yakushima taxa form a strongly supported clade. The chloroplast genome sequences and associated polymorphisms obtained in this study provide a foundation for subsequent studies on species delimitation, phylogeography, and population genetic structure and will enable future hypothesis testing regarding the independent origin and parallel adaptation of miniaturized Galium taxa on Yakushima Island.