CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Plant Biol. 2022 Aug 3;22(1):387. doi: 10.1186/s12870-022-03736-0.
Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.
The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.
This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.
姜兰属（姜兰科，姜兰科）是一个分布在亚洲和非洲的泛热带属。其物种在经济、观赏和药用价值方面具有重要意义。然而，由于有限和混淆的划界特征，姜兰属（姜兰属、头兰属和 Phaius）的分类学尚未得到充分解决。此外，有限的基因组信息显示其系统发育和系统发育存在不一致性。在这项研究中，我们使用 illumina 平台测序，进行从头组装，并对 8 种姜兰组物种的质体进行了比较分析：6 种姜兰属和 2 种 Phaius 种。系统发育分析用于重建物种之间以及与其他兰科植物的关系。
姜兰组物种的完整质体具有四分体结构，大小在 150,105bp-158,714bp 之间变化，包括一个大的单拷贝区（LSC；83,364bp-87,450bp）、一个小的单拷贝区（SSC；16,297bp-18,586bp）和一对反向重复区（IRs；25,222bp-26,430bp）。这些质体的总 GC 含量在 36.6-36.9%之间。这些质体编码了 131-134 个差异基因，其中包括 85-88 个蛋白编码基因、37-38 个 tRNA 基因和 8 个 rRNA 基因。比较分析表明，它们的序列、基因内容、基因顺序、序列重复和 GC 含量没有显著差异，因此高度保守。然而，在 C. delavayi（P. delavayi）中有些基因丢失了，包括 ndhC、ndhF 和 ndhK 基因。与编码区相比，非编码区具有更多的序列重复，因此对物种 DNA 条形码很重要。系统发育分析显示姜兰组具有并系关系，并证实了 Phaius delavayi 在姜兰属中的位置，而不是之前在 Phaius 属中的位置。
本研究提供了 6 种姜兰属和 2 种 Phaius 属物种完整质体的报告，并阐明了质体的结构特征。它还强调了质体数据在解决系统发育关系和阐明近缘物种分类学争议方面的强大功能，以提高我们对其系统发育和进化的理解。此外，它还为研究兰花物种的进化关系和群体遗传学提供了有价值的遗传资源和基础。
