Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Int J Mol Sci. 2023 Dec 22;25(1):184. doi: 10.3390/ijms25010184.
, commonly known as Darwin's orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine-cytosine (GC) content of 36.6-36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (-, -, -, - and -) and five protein-coding genes (, , , , and ) were identified. The consistent and robust phylogenetic relationships of were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for .
, 俗称达尔文兰花，是杓兰属（兰科）中最大的属。该属表现出高度的形态多样性，是进行宏观进化研究的良好候选对象。在这项研究中，首次报道了 4 个完整的叶绿体基因组，并探讨了潜在的变异性热点。叶绿体基因组具有典型的四分体结构，长度在 150743 到 151818 碱基对（bp）之间，鸟嘌呤-胞嘧啶（GC）含量为 36.6-36.9%。叶绿体基因组均包含 120 个基因，由 74 个蛋白编码基因（CDS）、38 个转移 RNA（tRNA）基因和 8 个核糖体 RNA（rRNA）基因组成；所有基因均为假基因或丢失。共鉴定出 30 到 46 个长重复序列和 55 到 63 个简单重复序列（SSR）。相对同义密码子使用（RSCU）分析表明密码子使用偏好具有高度保守性。大多数基因的 Ka/Ks 比值均低于 1，表明它们经历了纯化选择。基于核苷酸多样性（Pi）值的排序，鉴定出 5 个区域（-、-、-、-和-）和 5 个蛋白编码基因（、、、、和）。基于总共 40 个来自 Epidendroideae 亚科的叶绿体基因组，建立了 的一致且稳健的系统发育关系。杓兰属被强烈支持为一个单系群，与 Aeridinae 互为姐妹群。我们的研究为 的分子鉴定、叶绿体基因组进化和 DNA 条形码提供了理想的系统。
