Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, College of Horticulture, Hainan University, Haikou 570228, China.
Genes (Basel). 2022 Nov 4;13(11):2028. doi: 10.3390/genes13112028.
, which belongs to the family Araliaceae, is an endemic and endangered species of Hainan Island, China. It has potential economic and medicinal value owing to the presence of phenylpropanoids, flavonoids, triterpenoids, etc. The analysis of the structure and characteristics of the chloroplast genome (cpDNA) is crucial for understanding the genetic and phylogenetic evolution of this species. In this study, the cpDNA of was sequenced for the first time using next-generation sequencing methods, assembled, and annotated. We observed a circular quadripartite structure comprising a large single-copy region (86,440 bp), a small single-copy region (18,075 bp), and a pair of inverted repeat regions (25,944 bp). The total length of the cpDNA was 156,403 bp, and the GC% was 37.99%. We found that the chloroplast genome comprised 131 genes, with 86 protein-coding genes, 8 rRNA genes, and 37 tRNAs. Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the cpDNA. The most common amino acid encoded was leucine, with a strong A/T preference at the third position of the codon. The prediction of RNA editing sites in the protein-coding genes indicated that RNA editing was observed in 19 genes with a total of 54 editing sites, all of which involved C-to-T transitions. Finally, the cpDNA of 11 species of the family Araliaceae were selected for comparative analysis. The sequences of the untranslated regions and coding regions among 11 species were highly conserved, and minor differences were observed in the length of the inverted repeat regions; therefore, the cpDNAs were relatively stable and consistent among these 11 species. The variable hotspots in the genome included , , , , , , , , and , providing valuable molecular markers for species authentication and regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. Evolutionary selection pressure analysis indicated that the gene was strongly subjected to positive environmental selection. Phylogenetic analysis indicated that and were the most closely related species within the genus, and was closely related to the genera and in the Araliaceae family. Overall, the cp genomes reported in this study will provide resources for studying the genetic diversity and conservation of the endangered plant , as well as resolving phylogenetic relationships within the family.
落羽杉，隶属于五加科，是中国海南岛特有的濒危物种。由于存在苯丙素类、类黄酮类、三萜类等物质，它具有潜在的经济和药用价值。分析叶绿体基因组（cpDNA）的结构和特征对于了解该物种的遗传和系统发育进化至关重要。在这项研究中，我们首次使用下一代测序方法对落羽杉的 cpDNA 进行了测序、组装和注释。我们观察到一个圆形的四分体结构，由一个大的单拷贝区（86440 bp）、一个小的单拷贝区（18075 bp）和一对反向重复区（25944 bp）组成。cpDNA 的总长度为 156403 bp，GC%为 37.99%。我们发现，落羽杉的叶绿体基因组包含 131 个基因，其中 86 个是蛋白质编码基因，8 个 rRNA 基因，37 个 tRNA 基因。此外，我们在落羽杉的 cpDNA 中鉴定出了 26514 个密码子、13 个重复序列和 43 个简单序列重复位点。最常见的编码氨基酸是亮氨酸，密码子的第三位有很强的 A/T 偏好性。蛋白质编码基因中 RNA 编辑位点的预测表明，在 19 个基因中观察到了 RNA 编辑，共有 54 个编辑位点，均涉及 C 到 T 的转换。最后，我们选择了五加科的 11 个物种进行 cpDNA 比较分析。11 个物种的非翻译区和编码区序列高度保守，仅在反向重复区的长度上存在较小差异；因此，这 11 个物种的 cpDNA 相对稳定且一致。基因组中的可变热点包括、、、、、、、和，为物种鉴定和系统发育关系推断以及进化研究提供了有价值的分子标记。进化选择压力分析表明，基因受到了强烈的环境选择压力。系统发育分析表明，和是属内最密切相关的物种，而在五加科中与和属关系最为密切。总的来说，本研究报告的 cp 基因组将为研究濒危植物落羽杉的遗传多样性和保护以及解决科内的系统发育关系提供资源。
