Structural characteristics of the Phoebe hui chloroplast genome and phylogenetic analyses of Phoebe plants

In this study, the chloroplast genome of Phoebe hui was sequenced and assembled, and comparative analyses with those of other Phoebe plants were conducted, with a focus on variations in inverted repeat boundary variations, nucleotide diversity, selection pressure, codon usage bias, and phylogenetic relationships. The length of the chloroplast genome of P. hui exhibited a conserved size of 152,831 bp, the GC content was 39%, and the number of genes was 126; all the genes maintained a quadripartite circular structure. Significant interspecific variations in the inverted repeat boundary were observed; ndhF in P. hui resided entirely within the small single-copy region, while the extended ψycf1 of P. zhennan overlapped with ndhF by 637 bp and served as a potential molecular marker for species identification. Noncoding regions showed higher nucleotide diversity, with hypervariable regions identified as valuable tools for population genetics. Ka/Ks analysis revealed strong purifying selection on photosynthesis-related genes (psbA and rbcL), whereas stress-response genes (ndhF and ndhD) exhibited elevated synonymous substitution rates. A preference for A/U-ending codons was noted, although P. hui exhibited unique codon avoidance, suggesting translational optimization. Divergence time estimation indicated that Phoebe diverged from Machilus approximately 42.366 million years ago (Mya), P. hui diverged from its congeners approximately 24.916 Mya, and the most recent divergence occurred between P. bournei and P. chekiangensis at approximately 0.113 Mya. These divergence events may be associated with major geological events and Quaternary climatic fluctuations. This study provides genomic insights into the phylogeny of conserved endangered plants and the development of molecular markers for hybrid breeding.