Santalum (Santalaceae, sandalwood) is a hemiparasitic genus that includes approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of phylogenetic relationships will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. The Santalum chloroplast genome contains typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 110 unique genes. The whole set of ndh genes and the infA gene were found to lose their functions. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Branch-model-based selection analyses showed that the Santalum species were under widespread purifying selection. Our phylogenomic assessment provides an improved resolution to the phylogenetic relationships of Santalum compared to the past analyses. Our divergence time analysis showed that the crown age of Santalum was 8.46 Mya (million years ago), the first divergence occurred around 6.97 Mya, and diversification was completed approximately 1 Mya. By sequencing the 11 Santalum species chloroplast genomes, we identified the variations in the Santalum chloroplast genomes. Using the chloroplast genome sequences, phylogeny and divergence time analyses discovered that the Santalum species were likely to originate due to radiation evolution, and most speciation events occurred less than 1 Mya.

Agarwood is the dark resinous heartwood of injured ordinary Aquilaria sinensis (OA). Recently, some new clones of A. sinensis (Qi-Nan) that intensively produce high-quality agarwood were selected and cultivated by grafted clonal seedlings. However, very little is known about their agarwood formation mechanism, and it is unclear whether the current method of distinguishing Qi-Nan from OA by observing its leaf apparent morphology is scientifically reliable. In this study, the differences between OA and Qi-Nan clones in agarwood formation and their correlation with morphological, anatomical and physiological characteristics were investigated in two types of A. sinensis trees. After the mechanical injury, agarwood yield and essential oil content in agarwood of Qi-Nan were significantly higher than that of OA. There was no significant difference in leaf shape parameters between Qi-Nan and OA, but Qi-Nan showed higher specific leaf weight, total leaf chlorophyll, leaf nitrogen content and net photosynthetic rate. A xylem anatomical analysis showed that Qi-Nan had significantly smaller vessel wall thickness, greater ray cell wall thickness and larger interxylary phloem area than OA. Moreover, Qi-Nan had a greater consumption of non-structural carbohydrates than OA. Agarwood yield and oil content in agarwood showed significantly positive correlations with leaf photosynthetic capacity, the wall thickness of xylem ray cell, interxylary phloem area, starch utilization rate of trees, and a significantly negative correlation with the wall thickness of xylem vessel of trees. In brief, Qi-Nan has a stronger photosynthetic basis to supply more carbon sources, a more efficient xylem structural basis for agarwood production and a higher carbon source utilization rate, leading to a higher agarwood yield and oil content. It is not reliable to distinguish Qi-Nan from OA simply by observing leaf apparent morphology.

Sandalwood is one of the most expensive woods in the world and is well known for its long-lasting and distinctive aroma. In our study, chromosome-level genome assemblies for two sandalwood species (Santalum album and Santalumyasi) were constructed by integrating NGS short reads, RNA-seq, and Hi-C libraries with PacBio HiFi long reads. The S. album and S. yasi genomes were both assembled into 10 pseudochromosomes with a length of 229.59 Mb and 232.64 Mb, containing 21,673 and 22,816 predicted genes and a repeat content of 28.93% and 29.54% of the total genomes, respectively. Further analyses resolved a Santalum-specific whole-genome triplication event after divergence from ancestors of the Santalales lineage Malania, yet due to dramatic differences in transposon content, the Santalum genomes were only one-sixth the size of the Malania oleifera genome. Examination of RNA-seq data revealed a suite of genes that are differentially expressed in haustoria and might be involved in host hemiparasite interactions. The two genomes presented here not only provide an important comparative dataset for studying genome evolution in early diverging eudicots and hemiparasitic plants but will also hasten the application of conservation genomics for a lineage of trees recovering from decades of overexploitation.