Li Yu, Zheng Si-Si, Kozlowski Gregor, Song Yi-Gang
Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, Fribourg, Fribourg, 1700, Switzerland.
BMC Plant Biol. 2025 Aug 19;25(1):1098. doi: 10.1186/s12870-025-07072-x.
Quercus, as the most abundant and widely distributed genus within the family Fagaceae, has been extensively studied at nuclear genome and plastome. However, mitogenome studies in Quercus remain scarce. In this study, we assemble and annotate the mitogenome of Quercus gilva based on Illumina and Nanopore data. Additionally, we explore the structural features of its mitogenome and provide comprehensive analyses of the phylogeny and evolution of Fagaceae.
The Q. gilva mitogenome consists of four molecules (three circular molecules and one linear molecule) with 490,015 bp in total length and 45.68% in guanine-cytosine (GC) content. The mitogenome encodes 59 genes, including 37 protein-coding genes (PCGs), 19 transfer RNA genes (tRNAs), and three ribosomal RNA genes (rRNAs). We also examine the repeat sequences, codon usage bias, RNA editing sites, and endosymbiotic gene transfer in the mitogenome. The wide distribution of repeat sequences is a key factor in mitogenome rearrangement. These is widespread gene transfer among the mitogenome, plastome, and nuclear genome of Q. gilva. Comparative genomic analyses of the 11 Fagaceae mitogenomes reveal significant structural variations in size and gene loss. Synteny analysis further indicates extensive genome rearrangements and inversions within the 11 mitogenomes. However, analyses of nucleotide diversity (Pi) and nonsynonymous and synonymous substitution ratio (Ka/Ks) values reveal a low rate of evolution in the mitogenomes of Fagaceae. Finally, phylogenetic analysis based on 12 conserved mitochondrial PCGs of 40 taxa strongly supports the classification of Fabids.
In this study, the mitogenome of Q. gilva is newly assembled, providing important genomic resources for the phylogeny, resource conservation and development of Quercus. At the same time, the study of structural variation among the mitogenomes of Fagaceae species also help to elucidate the formation mechanism of mitogenome structural diversity.
栎属是壳斗科中数量最多、分布最广的属，已在核基因组和质体基因组方面得到广泛研究。然而，栎属的线粒体基因组研究仍然匮乏。在本研究中，我们基于Illumina和Nanopore数据组装并注释了枹栎的线粒体基因组。此外，我们探究了其线粒体基因组的结构特征，并对壳斗科的系统发育和进化进行了全面分析。
枹栎线粒体基因组由四个分子（三个环状分子和一个线性分子）组成，全长490,015 bp，鸟嘌呤-胞嘧啶（GC）含量为45.68%。该线粒体基因组编码59个基因，包括37个蛋白质编码基因（PCG）、19个转运RNA基因（tRNA）和三个核糖体RNA基因（rRNA）。我们还研究了线粒体基因组中的重复序列、密码子使用偏好、RNA编辑位点和内共生基因转移。重复序列的广泛分布是线粒体基因组重排的关键因素。枹栎的线粒体基因组、质体基因组和核基因组之间存在广泛的基因转移。对11个壳斗科线粒体基因组的比较基因组分析揭示了大小和基因丢失方面的显著结构变异。共线性分析进一步表明11个线粒体基因组内存在广泛的基因组重排和倒位。然而，核苷酸多样性（Pi）以及非同义替换与同义替换比率（Ka/Ks）值的分析表明壳斗科线粒体基因组的进化速率较低。最后，基于40个分类单元的12个保守线粒体PCG进行的系统发育分析有力地支持了蔷薇类植物的分类。
在本研究中，枹栎的线粒体基因组被重新组装，为栎属的系统发育、资源保护和开发提供了重要的基因组资源。同时，对壳斗科物种线粒体基因组结构变异的研究也有助于阐明线粒体基因组结构多样性的形成机制。
