Phylogeography of the Endangered Endemic Perkinsiodendron macgregorii Based on Chloroplast Genome Data

Perkinsiodendron macgregorii, an endangered Chinese endemic tree with high ornamental and ecological value, faces extinction threats due to its poor natural regeneration and habitat degradation. Despite the urgent need for its conservation, the genetic architecture and population differentiation mechanisms of this taxon remain poorly understood, hindering science-based protection strategies. We conducted comprehensive chloroplast genomic analyses of 134 individuals from 13 natural populations to inform science-based conservation. The chloroplast genome (158,538–158,641 bp) exhibited conserved quadripartite organization, with 113 functional genes and elevated GC contents in IR regions (42.99–43.02%). Population-level screening identified 741 SNPs and 678 indels, predominantly in non-coding regions (89.8%), with three distinct phylogeographic clades revealing north-to-south genetic stratification. The northern clade (Clade A) demonstrates the highest haplotype diversity and nucleotide diversity, followed by the southern clade (Clade C), while the central clade (Clade B) exhibits signals of genetic erosion (Tajima’s D > 3.43). Based on the genetic diversity distribution and phylogenetic tree of extant P. macgregorii, we inferred that the northern populations represent ancestral groups, while the Wuyi Mountains region and Nanling Mountains region served as glacial refugia. It is imperative to implement in situ conservation in these two regions. Additionally, ex situ conservation should involve collecting seed from representative populations across all three clades and establishing isolated cultivation lines for each clade. These findings establish a genomic framework for conserving endangered plants.