Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

Abstract

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.