Population genomic analyses provide insights on population structure and conservation strategies of incense tree Aquilaria sinensis

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values, and are now under threats from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, they are listed in the CITES Appendix II, which strictly regulates their international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 347 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbour-joining tree construction, ADMIXTURE and hierarchical pairwise-FST analyses suggested distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defence, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study. Resequencing of DNA extracted from two agarwood samples allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that subpopulation of incense tree in Hong Kong would require special conservation measures, and demonstrated the feasibility of utilising the established data for future conservation measures.