Sung Kyung HanP, Sang-Hyun Lee, Sung-Hyuk Park, Sung-Mo An,

Gumsung Cheon, Seungmin Lee, Jun-Gi ByeonC

Baekdudaegan Conservation Division, Baekdudaegan National Arboretum, Bonghwa, Korea

The genus Juniperus (Cupressaceae) shows complex species boundaries in Northeast Asia due to overlapping morphological traits and high ecological plasticity. To investigate plastome variation and phylogenetic relationships among Korean Juniperus taxa, we conducted a comparative analysis of complete chloroplast genomes. Seven complete plastomes were assembled from whole-genome sequencing, representing four described taxa (J. chinensis, J. chinensis var. sargentii, J. chinensis var. procumbens, and J. rigida), as well as additional Juniperus samples collected from Baekdu Mountain and Pohang. Plastome sizes ranged from 127,489 to 128,283 bp with conserved gene content (82 protein-coding, 33 tRNA, and 4 rRNA genes). A reduced inverted repeat (IR) region near duplicated trnQ-UUG genes (167–228 bp) was consistently detected, representing a major source of structural variation. Maximum-likelihood phylogenetic analyses generally recovered the separation of sect. Sabina and sect. Juniperus. J. chinensis and J. chinensis var. procumbens formed a clade, J. chinensis var. sargentii was recovered as a distinct lineage in plastome-based analyses, and the Baekdu Mountain sample clustered with J. sabina. These results highlight the usefulness of comparative chloroplast genome analyses for investigating phylogenetic relationships and evolutionary history within the genus Juniperus.