Yoo-Jung ParkP, Halam Kang, Hyeyeon Kim, Ji-Eun Park, Jae-Ein Choi, Kyeong-Sik CheonC

Department of Biological Science, Sangji University, Wonju, Korea

The chloroplast genome of the genus Adenophora exhibits remarkable structural variation, providing important information for evolutionary and taxonomic studies. In this study, we newly sequenced chloroplast genomes of nine taxa and performed comprehensive analyses of genome structure, repeat sequences, codon usage patterns, and phylogenetic relationships across a total of 19 Adenophora taxa, including 10 previously reported genomes. Comparative genomic analyses revealed nine distinct chloroplast genome structural types characterized by extensive large single copy (LSC) region rearrangements and inverted repeat (IR) boundary shifts. Repeat sequences were predominantly concentrated in the LSC region, with clear differences in the number and distribution patterns of repeat sequences among taxa. Codon usage analysis showed consistent genetic characteristics in most species, whereas A. himalayana and A. pinifolia exhibited unique patterns. Phylogenetic analyses using 76 protein-coding genes (CDS) through both concatenated and multi-locus species tree approaches revealed complex evolutionary relationships, and topological incongruence between the analytical methods suggests that resolving the evolutionary history of Adenophora remains a challenging task. Genome structural variations showed no clear correlation with infrageneric classification. This study provides new insights into the molecular evolutionary diversity of the genus Adenophora and is expected to serve as fundamental data for future comprehensive systematic research integrating nuclear DNA markers.

* This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education in 2024. (RS-2023-00243708).