Unraveling the phylogenetic position of a Korean endemic species Indigofera koreana (Fabaceae) through plastid genome analysis

Indigofera koreana is an endemic species to Korea, yet its phylogenetic position remains unresolved. In this study, we sequenced and analyzed plastid genomes (plastomes) to clarify the phylogenetic standing of I. koreana. We produced next-generation sequencing data for I. koreana and its close relative, Indigofera kirilowii. The plastomes of both species were successfully assembled, measuring 159,517 bp for I. kirilowii and 159,459 bp for I. koreana. Both species shared the same number of 128 intact genes and had identical 35.7% guanine–cytosine content. Phylogenetic analyses utilizing complete plastome and coding sequence–only data, along with 20 other Indigofera plastomes, were conducted to elucidate their evolutionary relationships. Our findings indicate that I. koreana forms a monophyletic group with Indigofera decora, Indigofera carlesii, and I. kirilowii, supported by maximum bootstrap values. Specifically, the phylogenetic tree derived from complete plastome data strongly suggests that I. koreana is most closely related to I. kirilowii. While these results are in line with previously suggested infra-generic classifications, they highlight the need for more comprehensive genomic studies to further unravel the evolutionary dynamics within the Indigofera genus, especially considering the role of polyploidization in species diversification.