Wang Ying, Zhan Di-Feng, Jia Xian, Mei Wen-Li, Dai Hao-Fu, Chen Xiong-Ting, Peng Shi-Qing
Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences Haikou, China.
College of Agronomy, Hainan University Haikou, China.
Front Plant Sci. 2016 Mar 8;7:280. doi: 10.3389/fpls.2016.00280. eCollection 2016.
Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal plant. Moreover, the results will enhance our understanding about the evolution of cp genomes of the Malvales order, particularly with regard to the role of A. sinensis in plant systematics and evolution.
白木香（Aquilaria sinensis (Lour.) Gilg）是一种重要的产沉香的药用木本植物，在传统中药中广泛应用。叶绿体（cp）基因组的高通量测序增进了对植物科内进化关系的理解。在本研究中，我们测定了白木香的完整cp基因组序列。白木香cp基因组大小为159,565 bp。该基因组包括一个87,482 bp的大单拷贝区域、一个19,857 bp的小单拷贝区域以及一对各为26,113 bp的反向重复序列（IRa和IRb）。基因组的GC含量为37.11%。白木香cp基因组编码113个功能基因，包括82个蛋白质编码基因、27个tRNA基因和4个rRNA基因。蛋白质编码基因中有7个基因重复，RNA基因中有11个基因重复。共鉴定出45个多态性简单序列重复位点和60对大重复序列。大多数简单序列重复位于大单拷贝/小单拷贝区域的非编码区，且A/T含量高。此外，33对大重复序列位于蛋白质编码基因中，27对位于基因间隔区。基于密码子使用情况，白木香cp基因组偏向于以A/T结尾。白木香cp基因组中密码子使用的分布与红柳桉（Gonystylus bancanus）cp基因组最为相似。对29种cp基因组的82个蛋白质编码基因的比较结果表明，在锦葵目内白木香是红柳桉的姐妹种。使用CGView比较工具，白木香cp基因组与红柳桉cp基因组的序列相似性最高，超过90%。这一发现有力地支持了将白木香置于锦葵目内作为红柳桉的姐妹种。完整的白木香cp基因组信息将对进一步研究这种传统药用植物非常有益。此外，这些结果将增进我们对锦葵目cp基因组进化的理解，特别是关于白木香在植物系统学和进化中的作用。
