Having great medicinal values, Dendrobium species of “Fengdou” (DSFs) are a taxonomically complex group in Dendrobium genus including many closely related and recently diverged species. Traditionally used DNA markers have been proved to be insufficient in authenticating many species of this group. Here, we investigated 101 complete plastomes from 23 DSFs, comprising 72 newly sequenced and 29 documented, which all exhibited well-conserved genomic organization and gene order. Plastome-wide comparison showed the co-occurrence of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), which can be explained by both the repeat-associated and indel-associated mutation hypotheses. Moreover, guanine-cytosine (GC) content was found to be negatively correlated with the three divergence variables (SNPs, indels and repeats), indicating that GC content may reflect the level of the local sequence divergence. Our species authentication analyses revealed that the relaxed filtering strategies of sequence alignment had no negative impact on species identification. By assessing the maximum likelihood (ML) trees inferred from different datasets, we found that the complete plastome and large single-copy (LSC) datasets both successfully identified all 23 DSFs with the maximum bootstrap values. However, owing to the high efficiency of LSC in species identification, we recommend using LSC for accurate authentication of DSFs.

“枫斗”石斛属植物（DSFs）具有很高的药用价值，是石斛属中一个分类复杂的类群，包括许多密切相关和最近分化的物种。传统使用的 DNA 标记已被证明不足以鉴定该组的许多物种。在这里，我们研究了来自 23 个 DSF 的 101 个完整质体，其中包括 72 个新测序的和 29 个已记录的质体，它们都表现出保守的基因组组织和基因顺序。全质体范围的比较显示单核苷酸多态性 (SNP) 和插入/缺失 (indels) 的共现，这可以通过重复相关和 indel 相关突变假设来解释。此外，发现鸟嘌呤胞嘧啶（GC）含量与三个分歧变量（SNP、插入缺失和重复）呈负相关，表明GC含量可能反映局部序列分歧的水平。我们的物种认证分析表明，宽松的序列比对过滤策略对物种识别没有负面影响。通过评估从不同数据集推断的最大似然 (ML) 树，我们发现完整的质体组和大型单拷贝 (LSC) 数据集均成功识别了具有最大引导值的所有 23 个 DSF。然而，由于LSC在物种鉴定方面的高效性，我们建议使用LSC来准确鉴定DSF。