Ma Dong, Tao Kaifeng, Xia Yanqiong, Luo Yan, Li Lu
College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China.
Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan, 650224, China.
BMC Genomics. 2025 Jul 2;26(1):632. doi: 10.1186/s12864-025-11791-8.
Brachycorythis Lindl. (Orchidinae, Orchidaceae) was characterized by a large and densely leafy stem throughout its length, comprising about 35 species with African-Asian disjunct distribution. However, the intergeneric and infrageneric phylogeny of Brachycorythis has been debated based on morphological and molecular data. The chloroplast (cp.) genomes of B. henryi and B. menglianensis were investigated in detail and compared with those of related taxa for providing new evidence for the phylogenetics of Brachycorythis.
The cp. genomes of B. henryi and B. menglianensis exhibited conserved quadripartite structures, measured 153,006 bp and 152,932 bp in length, with an identical GC content of 37.2%. Gene annotations identified 133 genes, 20 duplicated in the inverted repeat regions. Comparative analysis across their related species confirmed stable sequence identity and higher variation in single-copy regions. Phylogenetic analysis based on complete cp. genomic data revealed that these two Brachycorythis species formed an independent clade exhibiting distinct branch lengths, representing a sister lineage to their related taxa in Orchidinae s. s. It was also supported that six species of Brachycorythis formed a monophyletic clade based on matK + rbcL sequences. Among them, three species from Asia and other three species from Africa, respectively, formed two independent clades. Notably, it was also showed that B. macowaniana was not clustered with other six Brachycorythis species.
This is the first report on complete cp. genomic data of Brachycorythis, providing some phylogenetic implications. Some varied cp. genomic features for phylogenetic implications were discussed, including overall genome structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, and phylogenetic reconstruction. Based on chloroplast genomic data and matK + rbcL sequence analysis, phylogenetic results revealed that Brachycorythis was not closely related to any of the five genera assumed to be related. Three species from Asia and other three species from Africa, respectively, formed two independent clades, which was consistent well with the African-Asian disjunct distribution of Brachycorythis. And, it was supported that Gyaladenia should be re-established, considering the uncertain species of B. macowaniana. In addition, it was revealed that B. menglianensis was not a synonym of B. henryi, and each of them was a distinct species based on cp. genomic and morphological data. Therefore, the intergeneric and infrageneric relationship of Brachycorythis should be understood better by more cp. genomic data.
短筒兰属（Brachycorythis Lindl.，兰亚科，兰科）的特征是全株具大型且叶密集的茎，约有35个物种，呈非洲 - 亚洲间断分布。然而，基于形态学和分子数据，短筒兰属的属间和属下系统发育一直存在争议。详细研究了亨利短筒兰（B. henryi）和勐仑短筒兰（B. menglianensis）的叶绿体（cp.）基因组，并与相关类群的叶绿体基因组进行比较，为短筒兰属的系统发育提供新证据。
亨利短筒兰和勐仑短筒兰的cp.基因组呈现保守的四分体结构，长度分别为153,006 bp和152,932 bp，GC含量均为37.2%。基因注释确定了133个基因，其中20个在反向重复区域重复。对其相关物种的比较分析证实了单拷贝区域的序列同一性稳定且变异较高。基于完整cp.基因组数据的系统发育分析表明，这两个短筒兰物种形成了一个独立的分支，具有明显不同的分支长度，代表了兰亚科狭义范围内与其相关类群的姐妹谱系。基于matK + rbcL序列也支持短筒兰属的六个物种形成一个单系分支。其中，来自亚洲的三个物种和来自非洲的其他三个物种分别形成两个独立的分支。值得注意的是，还表明马氏短筒兰（B. macowaniana）未与其他六个短筒兰物种聚类。
这是关于短筒兰属完整cp.基因组数据的首次报道，提供了一些系统发育方面的启示。讨论了一些具有系统发育意义的不同cp.基因组特征，包括整体基因组结构、密码子使用、重复序列、IR边界、DNA多态性和系统发育重建。基于叶绿体基因组数据和matK + rbcL序列分析，系统发育结果表明短筒兰属与假定相关的五个属中的任何一个都没有密切关系。来自亚洲的三个物种和来自非洲的其他三个物种分别形成两个独立的分支，这与短筒兰属的非洲 - 亚洲间断分布非常一致。并且，考虑到马氏短筒兰物种的不确定性，支持应重新建立吉氏兰属（Gyaladenia）。此外，基于cp.基因组和形态学数据表明勐仑短筒兰不是亨利短筒兰的同义词，它们各自都是独特的物种。因此，通过更多的cp.基因组数据可以更好地理解短筒兰属的属间和属下关系。
