濒危紫皮石斛叶绿体基因组结构及系统发育分析

目的 解析紫皮石斛Dendrobium devonianum叶绿体基因组特征，并探讨石斛属系统发育关系。方法 采用Illumina技术对紫皮石斛进行测序，对其叶绿体基因组进行组装、注释和分析，并基于共有编码基因序列构建系统发育树。结果 紫皮石斛叶绿体基因大小为146 493 bp，总GC含量为37.4%；其大单拷贝区、小单拷贝区长度分别为84 932、13 036 bp，反向互补重复区为24 263 bp；共编码118个基因，包括72个蛋白质编码基因，38个tRNA基因和8个rRNA基因。密码子偏好分析表明，亮氨酸是紫皮石斛叶绿体基因组中使用频次最高的氨基酸。系统发育分析表明，紫皮石斛未形成单系，与兜唇石斛D.aphyllum构成姊妹关系；瘦轴组的重唇石斛D.hercoglossum和钩状石斛D.aduncum与石斛组其他物种聚为一支。结论 紫皮石斛叶绿体基因组呈典型四分体结构，其与兜唇石斛亲缘关系最近；瘦轴组的重唇石斛和钩状石斛与石斛组亲缘关系更近，并入石斛组更合理。

Analysis of chloroplast genome structure and phylogeny of endangered Dendrobium devonianum

Objective To obtain comprehensive information on the chloroplast (cp) genome of Dendrobium devonianum and estimate the phylogenetic relationships within the genus Dendrobium. Methods The cp genome of D. devonianum was sequenced using the Illumina platform. Bioinformatics software was employed to assemble, annotate, and characterize the cp genome. A phylogenetic tree was reconstructed based on the coding sequence. Results The complete cp genome of D. devonianum spaned 146 493 bp and consists of a large single-copy region (84 932 bp), a small single-copy region (13 036 bp), and reverse complementary repeat region (24 263 bp), and the total GC content was 37.4%. A total of 118 genes were identified, comprising 72 protein-coding genes, 38 tRNAs and 8 rRNAs. Analysis of codon usage bias revealed that leucine was the most frequently utilized amino acid in the cp genome. Phylogenetic analysis demonstrated that D. devonianum did not form a monophyletic clade instead of sharing a sister relationship with D. aphyllum. Additionally, D. hercoglossum and D. aduncum from Sect. Breviflores were grouped with other species from Sect. Dendrobium. Conclusion The cp genome of D. devonianum exhibits a typical circular tetrameric structure and displays the closest similarity to D. aphyllum. The D. hercoglossum and D. aduncum from Sect. Breviflores have a closer genetic relationship with the Sect. Dendrobium and it is more appropriate to incorporate them into the Sect. Dendrobium.