Gu Jiangmiao, Li Meijun, He Songtao, Li Zhi, Wen Fang, Tan Ke, Bai Xinxiang, Hu Guoxiong
College of Forestry, Guizhou University, Guiyang, 550025, China.
Biodiversity and Nature Conservation Research Center, Guizhou University, Guiyang, 550025, China.
Sci Rep. 2024 Dec 4;14(1):30256. doi: 10.1038/s41598-024-81524-6.
Guizhou Province is one of the most important karst regions of southwest China, with 22 Primulina species. These species are highly habitat-specialized and dependent on the soils of the karst region, and many inter-species classifications are unclear. Therefore, studying the chloroplast genomes and estimating the divergence times of there species can not only provide a better understanding of interspecific relationships but also help to know the species speciation and divergence in the karst environment. So, we sequenced and assembled the chloroplast genomes of nine Primulina species (including six endemic species of Guizhou) and conducted chloroplast genome comparison analysis and phylogenetic study. The chloroplast genome structures of the nine Primulina species were quadripartite with total lengths of 152,869-153,364 base pairs (bp) and GC content of 37.55-37.64%. There are 132 functional genes annotated, respectively. A total of 375 simple sequence repeats and 375 interspersed nuclear elements were identified. The 30 highly preferred codons identified were used at similar frequencies in different species, respectively. A phylogenetic tree constructed on the basis of the 38 chloroplast genomes showed that Primulina species form a monophyletic group. Eleven mutational hotspot regions that could serve as potential molecular markers were identified, of which two regions near the 3' and 5' ends of the ycf1 gene were of appropriate size and can serve as molecular markers for phylogenetic studies of Primulina. The results of molecular clock analyses indicate that the three major branches of Primulina begin to diverge in the Miocene, and the number of species proliferated in the Pliocene and Pleistocene. Most of the species of Primulina in Guizhou Province were formed in the Pleistocene and rapidly diverged within a short period of time. This research study enriches the genetic resource information of Primulina and deepens the understanding of the phylogenetic relationships of the genus.
贵州省是中国西南地区最重要的喀斯特地区之一，有22种报春苣苔属植物。这些物种对栖息地高度特化，依赖喀斯特地区的土壤，许多物种间的分类尚不明确。因此，研究这些物种的叶绿体基因组并估计其分化时间，不仅可以更好地理解种间关系，还有助于了解喀斯特环境中的物种形成和分化。所以，我们对9种报春苣苔属植物（包括6种贵州特有种）的叶绿体基因组进行了测序和组装，并进行了叶绿体基因组比较分析和系统发育研究。这9种报春苣苔属植物的叶绿体基因组结构均为四分体，全长152,869 - 153,364碱基对（bp），GC含量为37.55 - 37.64%。分别注释了132个功能基因。共鉴定出375个简单序列重复和375个散在核元件。鉴定出的30个高度偏好密码子在不同物种中分别以相似的频率使用。基于38个叶绿体基因组构建的系统发育树表明，报春苣苔属植物形成一个单系类群。鉴定出11个可作为潜在分子标记的突变热点区域，其中ycf1基因3'和5'端附近的两个区域大小合适，可作为报春苣苔属系统发育研究的分子标记。分子钟分析结果表明，报春苣苔属的三个主要分支在中新世开始分化，物种数量在上新世和更新世激增。贵州省的大多数报春苣苔属物种形成于更新世，并在短时间内迅速分化。本研究丰富了报春苣苔属的遗传资源信息，加深了对该属系统发育关系的理解。
