Complete chloroplast genome sequences of two miniaturized Galium species (Rubiaceae) from Yakushima Island, Japan
Abstract
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.
Related
- The complete chloroplast genome of diploid Hieracium tomentosum (Asteraceae, Cichorieae)
- The complete chloroplast genome of Rudbeckia hirta L. (Asteraceae) and its phylogenetic analysis
- The complete chloroplast genome of Melastoma dendrisetosum (melastomataceae), a shrub endemic to Hainan island, China
- The complete chloroplast genome of Erigeron sumatrensis (Asteraceae): genomic features and phylogenetic implications
- The complete chloroplast genome and phylogenetic analysis of Astragalus floridulus Podlech 1993 (Fabaceae)
BibTeX
@article{ishibashi2026complete,
title = {{Complete chloroplast genome sequences of two miniaturized Galium species (Rubiaceae) from Yakushima Island, Japan}},
author = {Masamitsu Ishibashi and Eiji Gotoh and Yoshihisa Suyama and Daiki Takahashi},
journal = {Plant Biotechnology},
year = {2026},
month = sep,
doi = {10.5511/plantbiotechnology.26.0313b},
url = {https://www.jstage.jst.go.jp/article/plantbiotechnology/43/3/43_26.0313b/_article},
note = {CC BY},
}
RIS
TY - JOUR
TI - Complete chloroplast genome sequences of two miniaturized Galium species (Rubiaceae) from Yakushima Island, Japan
AU - Masamitsu Ishibashi
AU - Eiji Gotoh
AU - Yoshihisa Suyama
AU - Daiki Takahashi
PY - 2026
DA - 2026/09/25
JO - Plant Biotechnology
DO - 10.5511/plantbiotechnology.26.0313b
UR - https://www.jstage.jst.go.jp/article/plantbiotechnology/43/3/43_26.0313b/_article
AB - 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.
SN - 1347-6114
SN - 1342-4580
ER -