The Complete Chloroplast Genome of the Vietnamese Endemic Species P.H. Hô, 1986 (Thymelaeaceae): Structure, Evolution, and Phylogeny.

The genus (Thymelaeaceae) is renowned for producing agarwood, a highly valuable resinous product of significant economic and cultural value. Yet, many of its species, including the endemic from Vietnam, face conservation challenges due to overexploitation. This study presents the first complete chloroplast (cp) genome of to investigate its genome structure, evolutionary characteristics, and phylogenetic position. The cp genome of . was 174,810 bp, exhibiting a typical quadripartite structure with a large single-copy (LSC) region (87,264 bp), a small single-copy (SSC) region (3342 bp), and two inverted repeat (IR) regions (42,102 bp), encoding unique 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analysis across species revealed conserved genomic features, including IR expansion into the SSC region, absence of introns, alongside moderate nucleotide divergent regions (such as -, , , and ) and a distinct variant in . Phylogenetic reconstruction using whole cp genomes of 13 species placed sister to mainland Southeast Asian species like and , clearly separated from insular Southeast Asian groups. The correlation between phylogenetic structure and geographic distribution suggests that historical biogeography and ecological factors have driven lineage divergence in . These findings highlight the genetic distinctiveness of and provide valuable genetic resources for species identification and conservation planning for this vulnerable species.