Organelle genome analysis reveals adaptation and conservation in endangered tree Phoebe chekiangensis

Phoebe chekiangensis, a nationally protected tree endemic to southeastern China, is of high ecological and economic value but lacks genomic resources for conservation and evolutionary studies. In this study, we assembled its complete organelle genomes, including a circular mitogenome of 864,971 bp and a plastome of 154,460 bp. The mitogenome is enriched in dispersed and simple sequence repeats, consistent with extensive structural rearrangements across Lauraceae, whereas coding regions (over 80 % similarity) remain largely collinear under strong functional constraints. We identified 31 mitochondrial plastid DNA sequences (26,890 bp; 3.11 % of the mitogenome), including five intact plastid protein-coding genes (PCGs) and 14 tRNAs, reflecting frequent plastid-to-mitochondrion transfers that may restore missing tRNAs and enhance genome variability. RNA editing analysis revealed 71 mitochondrial and 13 plastid sites, with cox1 harboring the most, suggesting post-transcriptional modification of respiratory genes that could contribute to stress tolerance. Comparative analyses showed that plastid PCGs evolve faster than mitochondrial PCGs, and atp6 displayed a signal of positive selection, potentially linked to adaptive adjustments in ATP synthase function and respiratory efficiency. Phylogenetic analyses based on organelle genomes confirmed the monophyly of Lauraceae but revealed little topological conflicts, likely reflecting lineage-specific substitution-rate heterogeneity. In conclusion, our results provide new insights into the dynamics of organelle genome evolution and establish valuable genomic resources for the conservation and molecular systematics of P. chekiangensis and Lauraceae.