Zou Yi, Zhu Weidong, Hou Yingke, Sloan Daniel B, Wu Zhiqiang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Genome Biol. 2025 Aug 11;26(1):240. doi: 10.1186/s13059-025-03717-0.
In plants, comparative analyses of organellar genomes are often based on draft assemblies. Large-scale investigations into the complex structural rearrangements of mitochondrial genomes remain scarce.
Here, we perform a comprehensive analysis of the dominant conformations and dynamic heteroplasmic variants of organellar genomes in the model plant Arabidopsis thaliana, utilizing high-quality long-read assemblies validated at high resolution from 149 samples. We find that mitochondrial and plastid genomes share common types of structural and small-scale variants driven by similar DNA sequence features. However, rearrangements mediated by repetitive sequences in mitochondrial genomes evolve so rapidly that they are often decoupled from other types of variants. Rare complex events involving elongation and fusion of existing repeats are also observed, contributing to the unalignable regions commonly found at the interspecies level. Additionally, we demonstrate that disrupting and rescuing organellar DNA maintenance could drive the rapid evolution of dominant mitochondrial genome conformations.
Our study provides an unprecedentedly detailed view of the dynamics of organellar genomes at pan-genome scale in Arabidopsis thaliana, paving the way to unlock the full potential of organellar genetic resources.
在植物中，细胞器基因组的比较分析通常基于草图组装。对线粒体基因组复杂结构重排的大规模研究仍然很少。
在这里，我们利用从149个样本中经过高分辨率验证的高质量长读段组装，对模式植物拟南芥细胞器基因组的主要构象和动态异质性变体进行了全面分析。我们发现线粒体和质体基因组共享由相似DNA序列特征驱动的常见结构和小规模变体类型。然而，线粒体基因组中由重复序列介导的重排进化得非常快，以至于它们常常与其他类型的变体解耦。还观察到涉及现有重复序列的延伸和融合的罕见复杂事件，这导致了种间水平常见的无法比对区域。此外，我们证明破坏和挽救细胞器DNA维持可以驱动主要线粒体基因组构象的快速进化。
我们的研究以前所未有的详细程度展示了拟南芥全基因组规模下细胞器基因组的动态变化，为释放细胞器遗传资源的全部潜力铺平了道路。
