Wang Yunsheng, Shahid Muhammad Qasim
School of Health and Life Science, Kaili University, Kaili, Guizhou, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
Front Plant Sci. 2023 Jan 4;13:1035157. doi: 10.3389/fpls.2022.1035157. eCollection 2022.
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Blume () (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. () and () are two common forms that naturally grow in different habitats with difference in altitude and latitude. () often occurs sporadically in cultivated populations of and . However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of and have not been revealed. Here, we assembled a chromosome-level draft genome of with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 accessions, nine accessions, and 10 accessions, and identified two independent genetic lineages: _pedigree ( individuals and individuals collected from populations) and _pedigree ( individuals and individuals collected from populations), which strongly support the taxonomic status of and as subspecies, not as different forms. In highly differentiated genomic regions of _pedigree and _pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between _pedigree and _pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of and the new findings would deepen the understanding about ecological adaptation and evolution of .
水平基因转移在高等植物中是一种罕见且有用的遗传机制。虾脊兰（Blume）（兰科），作为东亚著名的传统药材，采用异养生活方式，因此被认为更容易发生水平基因转移（HGT）。虾脊兰是一个“多型种”，目前根据植物形态分为五个公认的类型。台湾虾脊兰（Calanthe formosana）和三棱虾脊兰（Calanthe tricarinata）是两种常见类型，自然生长在不同的栖息地，海拔和纬度存在差异。台湾虾脊兰（Calanthe formosana）经常零星出现在虾脊兰（Calanthe discolor）和三棱虾脊兰（Calanthe tricarinata）的栽培种群中。然而，支撑台湾虾脊兰（Calanthe formosana）和三棱虾脊兰（Calanthe tricarinata）不同生态适应性的遗传关系和遗传机制尚未揭示。在此，我们组装了一个大小为1.04 Gb的虾脊兰染色体水平基因组草图。在预测的17,895个蛋白质编码基因中，我们鉴定出三个水平基因转移事件。同时，我们对10个台湾虾脊兰（Calanthe formosana）样本、9个虾脊兰（Calanthe discolor）样本和10个三棱虾脊兰（Calanthe tricarinata）样本进行了重测序，并鉴定出两个独立的遗传谱系：formosana谱系（从台湾虾脊兰（Calanthe formosana）种群收集的20个个体和10个个体）和tricarinata谱系（从三棱虾脊兰（Calanthe tricarinata）种群收集的20个个体和10个个体），这有力地支持了台湾虾脊兰（Calanthe formosana）和三棱虾脊兰（Calanthe tricarinata）作为亚种而非不同类型的分类地位。在formosana谱系和tricarinata谱系高度分化的基因组区域中，在选择扫描基因组区域鉴定出三个编码查尔酮合酶的基因和一个编码生长素（AUX）/吲哚乙酸（IAA）的Phox/Bem1p（PB1）结构域，这表明formosana谱系和tricarinata谱系之间的分化是由与光反应以及生长和发育相关的基因选择所促进的。总体而言，这个新基因组将有助于虾脊兰的育种和利用，新发现将加深对虾脊兰生态适应性和进化的理解。
