Forest Biotechnology Laboratory, Department of Forestry Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900, Sepang, Selangor, Malaysia.
Sci Rep. 2020 Aug 3;10(1):13034. doi: 10.1038/s41598-020-70030-0.
Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
沉香树物种自然分布于印度-马来亚地区，受到过度开发的保护。它们产生一种具有高经济价值的芳香非木材产品，即沉香。沉香属植物种间界限模糊，遗传信息有限，这是保护工作的障碍之一。在这项研究中，我们对 8 个沉香属物种的完整叶绿体基因组进行了比较分析，其中 7 个是使用 Illumina HiSeq X Ten 平台进行新测序并进行从头组装的。沉香属叶绿体基因组具有典型的四分体结构，包括基因顺序和基因组结构。每个 cp 基因组的长度约为 174 kbp，编码 89 到 92 种蛋白质、38 种 tRNA 和 8 种 rRNA，其中 27 种在 IR（反向重复）区重复。此外，还鉴定了 832 个重复（正向、反向、回文和互补重复）和 9 个高度可变区。系统发育分析表明，沉香属 cp 基因组的拓扑结构在基于 cp 基因组数据集的情况下得到了很好的呈现，并且与它们的地理分布模式相匹配。总之，完整的 cp 基因组将有助于开发特定于物种的分子工具来区分沉香属物种，并解决瑞香科成员的进化关系。
