Chloroplast genome analysis and divergence time estimation of 11 Dendrobium officinale(11种铁皮石斛叶绿体基因组分析及分化时间推算)

Examining the genetic diversity of Dendrobium officinale from different geographical origins is crucial for advancing the understanding of the origin and evolutionary divergence of this species, and provides a valuable theoretical basis for the conservation of its germplasm resources. In the present study, the chloroplast genome structure and characteristics of 11 D. officinale species from different geographical origins were analyzed. The results indicated that all 11 chloroplast genomes had a quadripartite structure, with total lengths ranging from 152 018 bp to 152 250 bp. A total of 124-131 genes were annotated, including 76-80 protein-coding genes, 8 rRNA genes, and 37-38 tRNA genes. Base on the comparison of the large single copy/inverted repeat/small single copy (LSC/IR/SSC) boundary, sequence collinearity and simple sequence repeat (SSR) of 11 D. officinale chloroplast genomes, it was shown that the overall differences among the 11 D. officinale chloroplast genomes were small, despite some certain sequence inconsistencies. For example, the chloroplast genomes of Zhejiang D. officinale differed from those of the other 10 species in terms of the IRb/SSC boundary. Collinearity analysis using Yandang Mountain D. officinale as the reference genome revealed significant sequence differences in the IRb region compared with those in Taiwan D. officinale. Additionally, there were some differences in the number and types of SSR among the 11 D. officinale species. However, overall, the sequence differences were small, indicating a relatively slow evolutionary rate. The divergence time of 11 D. officinale from different geographical origins was estimated using molecular clock theory, which indicated that Yunnan D. officinale was the first to diverge, with a divergence time of 8.98 million years ago (Mya). Dendrobium officinale from Yandang Mountain, Taiwan, Guangxi, Guizhou, Zhejiang, Fujian, Guangdong, Hunan, and Jiangxi subsequently diverged in sequence. Huoshan (Anhui) D. officinale diverged last, at 0.02 Mya. These results indicate that the 11 D. officinale species exhibit minor sequence differences, conserved sequences, and relatively slow evolutionary rates. The genetic relationships among D. officinale from different regions are close in this investigation, and the cultivation backgrounds are indistinct, possibly due to mutual introduction among different regions, or it may be that certain production areas possess unique geographical conditions during the natural evolutionary process, leading to increased susceptibility to variation in D. officinale within these areas. . 研究不同产地来源的铁皮石斛（Dendrobium officinale）遗传差异性，有利于深入了解铁皮石斛物种起源与分化，为铁皮石斛种质资源的保护提供理论依据。本研究分析了11种不同产地来源的铁皮石斛叶绿体基因组结构及特征。结果表明：11种铁皮石斛叶绿体基因组均为四分体结构，总长度为152 018～152 250 bp，包含124～131个基因，其中蛋白编码基因76～80个，rRNA基因8个，tRNA基因37～38个。通过对比叶绿体基因组大单拷贝区（large single copy, LSC）/反向重复区（inverted repeat, IR）/小单拷贝区（small single copy, SSC）边界信息、序列共线性和简单重复序列发现，11种铁皮石斛叶绿体基因组整体差异度较小，但也存在一定的序列不一致性，如浙江铁皮石斛与其他10种铁皮石斛在IRb/SSC边界处显示出不同；以雁荡山铁皮石斛为参考基因组的共线性分析显示其与台湾铁皮石斛在IRb区域表现出较大的序列差异；同样，在简单重复序列的数量和种类上11种铁皮石斛也表现出一定的差异。利用分子钟原理推算显示，在本研究的11种铁皮石斛中，云南铁皮石斛最先分化形成，分化时间为8.98百万年前（million years ago, Mya），随后依次分化出现雁荡山、台湾、广西、贵州、浙江、福建、广东、湖南和江西等地铁皮石斛，安徽霍山铁皮石斛最后分化出现，时间为0.02 Mya。综上所述，本研究的11种铁皮石斛序列差异小且保守、进化速率相对较慢。不同地域之间铁皮石斛亲缘关系较近、种植背景模糊，可能与不同地域相互引种有关，也可能是在自然演化过程中部分产地地理条件特殊，使得该产地铁皮石斛更容易发生变异。