Abstract
The genus Aquilaria (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 Aquilaria banaense from Vietnam, face conservation challenges due to overexploitation. This study presents the first complete chloroplast (cp) genome of A. banaense to investigate its genome structure, evolutionary characteristics, and phylogenetic position. The cp genome of A. banaense 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 Aquilaria species revealed conserved genomic features, including IR expansion into the SSC region, absence of clpP1 introns, alongside moderate nucleotide divergent regions (such as matK-rps16, petN-trnT-GGU, rps4-ndhJ, and ndhF-rpl32) and a distinct accD variant in A. banaense. Phylogenetic reconstruction using whole cp genomes of 13 Aquilaria species placed A. banaense sister to mainland Southeast Asian species like A. crassna and A. subintegra, 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 Aquilaria. These findings highlight the genetic distinctiveness of A. banaense and provide valuable genetic resources for species identification and conservation planning for this vulnerable species.