Wan Tian, Qiao Bai-Xue, Zhou Jing, Shao Ke-Sen, Pan Liu-Yi, An Feng, He Xu-Sheng, Liu Tao, Li Ping-Ke, Cai Yu-Liang
College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China.
College of Natural Resources and Environment, Northwest Agriculture & Forestry University, Yangling, China.
Front Plant Sci. 2023 Mar 3;14:1070600. doi: 10.3389/fpls.2023.1070600. eCollection 2023.
The subgenus , one of the most important groups in the genus , comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known species. Here, we report the chloroplast (cp) genome sequences of 11 species to provide insight into evolution of the plastome. The cp genomes of the 11 species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including , , , -, -, and -. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the , , , and genes; whereas , , , , and showed a signature of possible positive selection during the course of evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which was separated as an independent subclade. was genetically closer to , , and () than to members of true cherry, whereas and were most closely related to and . However, formed a clade with , , × 'Gisela 6', and as a true cherry group. These results provide new insights into the plastome evolution of , along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of species.
该亚属是该属中最重要的类群之一，包含100多个物种；然而，其分类地位和系统发育关系仍存在争议。因此，有必要重建已知物种的系统发育树。在此，我们报告了11个该物种的叶绿体（cp）基因组序列，以深入了解质体基因组的进化。这11个物种的cp基因组（157,571 - 158,830 bp）呈现出典型的四分体环状结构。质体基因组包含115个独特基因，包括80个蛋白质编码基因、4个核糖体RNA和31个转运RNA。发现20个基因在反向重复序列以及边界处重复。与编码区相比，保守的非编码序列显示出显著差异。我们发现12个基因和14个基因间隔区具有较高的核苷酸多样性和更多的多态性位点，包括、、、 - 、 - 和 - 。在cp质体基因组进化过程中，密码子偏好性在第三位碱基强烈偏向使用A/T，亮氨酸和异亮氨酸密码子出现频率最高。我们在、、、和基因上鉴定出强烈的纯化选择；而、、、、和在进化过程中显示出可能的正选择特征。此外，我们进一步分析了这些物种与其他57个同属相关物种的系统发育关系。通过重建系统发育树，我们发现真樱桃与中国的植物区系相似，形成一个独特的类群，从中被分离为一个独立的亚分支。在遗传上与、、和（）比与真樱桃的成员更接近，而和与和关系最为密切。然而，与、、ב吉塞拉6’和作为一个真樱桃类群形成一个分支。这些结果为该物种的质体基因组进化提供了新的见解，同时为该物种进一步的系统发育和系统地理学分析提供了潜在的分子标记和候选DNA条形码。
