College of Life Sciences, Nanjing Normal University, Nanjing, China.
Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, China.
BMC Plant Biol. 2023 Nov 23;23(1):586. doi: 10.1186/s12870-023-04618-9.
Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses.
Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species.
Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels.
线粒体基因组对于破译种子植物独特的进化历史至关重要。然而，在大多数植物谱系中，其基因组大小、多染色体结构和外源序列的极端变异规律仍未得到解决，这进一步阻碍了线粒体基因组在系统发育分析中的应用。
本研究以形态差异大、物种分类困难的石斛属（兰科）为研究对象。我们首先从头组装了两个完整的铁皮石斛和河南石斛的线粒体基因组，它们分别长 763,005bp 和 807,551bp，具有多染色体结构。为了了解石斛属线粒体基因组的进化，我们将其与其他四个兰科物种的线粒体基因组进行了比较。结果表明，石斛属线粒体基因组中的重复序列和叶绿体来源序列存在很大差异。此外，石斛属线粒体基因组的基因间区在进化过程中发生了扩张。我们还对 26 种石斛属物种的线粒体基因组进行了新测序，并基于基因组线粒体和质体数据重建了石斛属的系统发育关系。结果表明，叶绿体来源序列的存在使得线粒体系统发育显示出线粒体系统发育的部分特征。此外，线粒体系统发育为石斛属物种的系统发育关系提供了新的见解。
本研究揭示了石斛属线粒体基因组的进化以及线粒体基因组在解析低分类水平系统发育关系方面的潜力。
