球茎是兰科最大的属之一,存在一些最复杂的分类学问题,包括具有观赏性和医学重要性的物种。缺乏有关Bulbophyllum叶绿体(cp)基因组表征的知识,对我们的研究施加了当前的限制。这里,我们报告了七种Bulbophyllum物种的完整cp基因组,包括B.ambrosia,B.crassipes,B.Farreri,B.Hamatum,B.shanicum,B.Triste,和紫罗兰B,并与相关分类群进行比较,以更好地了解其分类学和系统发育的基因组信息。共有28个Bulbophylumcp基因组表现出典型的四部结构,长度范围为145,092bp至165,812bp,GC含量为36.60%至38.04%。每个基因组包含125-132个基因,包括74-86个蛋白质编码基因,38个tRNA基因,和八个rRNA基因。基因组排列,基因含量,和长度相似,在ndh基因组成中观察到差异。值得注意的是,在B.crassipes的IR区域中存在外源片段插入。共检测到18-49个长重复序列和38-80个简单序列重复序列(SSR),单核苷酸(A/T)在Bulbophylumcp基因组中占优势,有明显的A/T偏好。对相对同义密码子使用(RSCU)的分析显示,亮氨酸(Leu)是最常用的密码子,而半胱氨酸(Cys)使用最少。六个高度可变区(rpl32-trnLUAG>trnTUGU-trnLUAA>trnFGAA-ndhJ>rps15-ycf1>rbcL-accD>psbI-trnSGCU)和五个编码序列(ycf1>rps12>matK>psbK>rps15)被鉴定为潜在的DNA标记基于核苷酸多样性。此外,在完整的cp基因组中鉴定出31,641个分子诊断特征(MDC)。基于完整的cp基因组序列和68个蛋白质编码基因的系统发育分析强烈支持28个Bulbophyllum物种可以分为四个分支,教派。Brachyantha,Cirrhopetalum,还有Leopardinae,由形态学定义,是非一成不变的。我们的研究结果丰富了Bulbophyllum的遗传资源,提供有价值的信息来说明复杂的分类法,系统发育,和该属的进化过程。
Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we report the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste, and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and a GC content of 36.60% to 38.04%. Each genome contained 125-132 genes, encompassing 74-86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents, and length were similar, with differences observed in ndh gene composition. It is worth noting that there were exogenous fragment insertions in the IR regions of B. crassipes. A total of 18-49 long repeats and 38-80 simple sequence repeats (SSRs) were detected and the single nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed that leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions (rpl32-trnLUAG > trnTUGU-trnLUAA > trnFGAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnSGCU) and five coding sequences (ycf1 > rps12 > matK > psbK > rps15) were identified as potential DNA markers based on nucleotide diversity. Additionally, 31,641 molecular diagnostic characters (MDCs) were identified in complete cp genomes. A phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported that 28 Bulbophyllum species can be divided into four branches, sects. Brachyantha, Cirrhopetalum, and Leopardinae, defined by morphology, were non-monophyly. Our results enriched the genetic resources of Bulbophyllum, providing valuable information to illustrate the complicated taxonomy, phylogeny, and evolution process of the genus.