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.

中文翻译：

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檀香（檀香科）完整叶绿体基因组的比较和系统发育分析

Santalum（檀香科，檀香）是一种半寄生属，包括大约 15 种现存物种。它以其芳香的心材油而闻名，用于熏香和香水。对檀香产品的需求导致过度采伐，野生檀香种群现在受到威胁。系统发育关系的知识对于该属的保护和适当管理至关重要。在这里，我们对 11 个Santalum物种的叶绿体基因组进行了测序。然后将这些数据用于研究Santalum和相关物种内的叶绿体基因组进化动力学和关系以及分化时间。该檀香叶绿体基因组包含典型的四分体结构，范围从 143,291 到 144,263 bp。叶绿体基因组包含 110 个独特的基因。整套的NDH基因和INFA基因被发现失去其功能。Santalum物种之间的 P 距离为 0.0003 至 0.00828。在Santalum叶绿体基因组中发现了三个突变热点区域、14 个小倒位和 460 个 indels 事件。基于分支模型的选择分析表明，Santalum物种处于广泛的净化选择之下。我们的系统发育评估为Santalum的系统发育关系提供了更好的解决方案与以往的分析相比。我们的分歧时间分析表明，Santalum的冠龄为 8.46 Mya（百万年前），第一次分歧发生在 6.97 Mya 左右，大约在 1 Mya 完成分化。通过对 11 个Santalum物种叶绿体基因组进行测序，我们确定了Santalum叶绿体基因组中的变异。使用叶绿体基因组序列、系统发育和分化时间分析发现，Santalum物种可能起源于辐射进化，并且大多数物种形成事件发生在 1 Mya 以内。