Shen Ruo-Han, Li Yu, Yang Liang-Hai, Zheng Si-Si, Yan Xu, Kozlowski Gregor, Dai Xi-Ling, Song Yi-Gang
College of Life Sciences, Shanghai Normal University, Shanghai, China.
Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
Front Plant Sci. 2025 Aug 19;16:1620373. doi: 10.3389/fpls.2025.1620373. eCollection 2025.
Compared to the large number of chloroplast genome resources in , only six mitogenomes (belonging to three sections) have been reported. To date, no mitogenome has been reported for section , a representative species whose chloroplast genome has been characterized, is an endangered tree endemic to the montane cloud forests of southern China.
In this study, we assembled and annotated the mitogenome of section () for the first time using the HiFi reads. We examined repeat sequences, codon usage bias, RNA editing events, and chloroplast to mitochondrion DNA transfer events, and performed collinearity analysis and phylogenetic analysis with other Fagaceae species.
The mitogenome of revealed a multipartite structure composed of three continuous segments with 516,686 bp in length. The genome encoded 38 protein-coding genes, 23 transfer RNA genes, and three ribosomal RNA genes. Repeat analysis uncovered diverse simple sequence repeats and interspersed sequences, and codon usage showed clear biases. Nonsynonymous sites of RNA editing showed 12 different effects on amino acids. Notably, a small amount (1.20%) of DNA sequences occurred gene transfer events between organelles in . Comparative synteny analysis revealed substantial structural variation among oak mitogenomes. was closely related to in both the mitochondrial and chloroplast trees.
This work fills a critical gap in mitochondrial genomic resources for section , and provides new insights into the structural diversity and evolutionary dynamics. It also establishes a valuable genomic foundation for phylogenetic reconstruction, adaptive evolution research, and the conservation of endangered species.
与大量的叶绿体基因组资源相比，仅报道了六个线粒体基因组（属于三个组）。迄今为止，尚未报道过组的线粒体基因组，是一种具有代表性的物种，其叶绿体基因组已得到表征，是中国南方山地云雾林中特有的濒危树种。
在本研究中，我们首次使用HiFi reads组装并注释了组的线粒体基因组。我们检查了重复序列、密码子使用偏好、RNA编辑事件以及叶绿体到线粒体的DNA转移事件，并与其他壳斗科物种进行了共线性分析和系统发育分析。
的线粒体基因组呈现出由三个连续片段组成的多部分结构，长度为516,686 bp。该基因组编码38个蛋白质编码基因、23个转运RNA基因和三个核糖体RNA基因。重复序列分析发现了多种简单序列重复和散布序列，密码子使用表现出明显的偏好。RNA编辑的非同义位点对氨基酸有12种不同的影响。值得注意的是，少量（1.20%）的DNA序列在的细胞器之间发生了基因转移事件。比较共线性分析揭示了栎属线粒体基因组之间存在大量结构变异。在线粒体和叶绿体系统发育树中均与密切相关。
这项工作填补了组线粒体基因组资源的关键空白，并为结构多样性和进化动态提供了新的见解。它还为系统发育重建、适应性进化研究和濒危物种的保护建立了有价值的基因组基础。
