Ma Yang, López-Pujol Jordi, Yan Dongqing, Deng Zekun, Zhou Zhen, Niu Jianming
School of Ecology and Environment, Inner Mongolia University, Hohhot, 010020, People's Republic of China.
Botanic Institute of Barcelona (IBB), CSIC-CMCNB, Barcelona, 08038, Spain.
BMC Genomics. 2025 Mar 31;26(1):314. doi: 10.1186/s12864-025-11474-4.
The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica).
A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465 bp and 1,539,836 bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (> 1000 bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS ≤ 70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively.
We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.
列当科被广泛认为是研究寄生植物进化动态的典范模型系统。然而，目前关于半寄生族齿鳞草族线粒体基因组（mitogenome）的报道尚缺。在此，我们对狭义齿鳞草属（蒙古齿鳞草和达乌里齿鳞草）的完整线粒体基因组进行了测序、组装和特征分析。
两种半寄生植物的线粒体基因组共有51个独特的线粒体基因，包括33个蛋白质编码基因、3个rRNA基因和15个tRNA基因，呈现出自养植物的基因含量特征。蒙古齿鳞草和达乌里齿鳞草的线粒体基因组以五环染色体结构（其主要构象）为特征，长度分别为1,576,465 bp和1,539,836 bp。此外，我们鉴定并验证了蒙古齿鳞草中由四对大重复序列（大小>1000 bp）介导的四种次要构象的存在，以及达乌里齿鳞草中由六对大重复序列介导的八种次要构象的存在。我们进一步探究了两种齿鳞草线粒体基因组中的密码子使用情况、RNA编辑位点、选择压力和核苷酸多样性。对唇形目26个物种的系统发育分析表明，两种齿鳞草物种形成了一个与列当科其他谱系的姐妹分支。在齿鳞草和五个近缘物种之间也观察到了广泛的线粒体基因组重排。虽然我们在齿鳞草线粒体基因组中鉴定到了线粒体质体序列（MTPTs），但其线粒体质体序列分别仅占2.37%和1.74%。此外，细胞内和水平基因转移的证据极少，只有少数基因（rpl22、rps3和ycf2）分别与潜在宿主植物蒙古葱、羊草和防风的关系显示出较低的自展支持率（BS≤70%）。
我们首次报道了半寄生齿鳞草属物种的线粒体基因组，其特征为多次重复介导的重组以及极少或没有细胞内和水平基因转移。我们的研究结果为进一步研究半寄生植物线粒体基因组进化提供了有价值的遗传见解。
