Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants.
Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants.
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DOI：
10.1111/tpj.15976
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发表时间：
2022-11
期刊：
影响因子：
7.2
通讯作者：
Wu, Zhiqiang
中科院分区：
文献类型：
--
作者：
Zou, Yi;Zhu, Weidong;Sloan, Daniel B.;Wu, Zhiqiang
关键词：
植物线粒体基因组中丰富的重复序列可以引起快速的基因组重排，也是短读段测序研究的主要障碍。已知核编码蛋白如MSH1抑制重复相关线粒体基因组变体的产生，但我们对这些机制的理解受到短读技术的限制。在这里，我们使用高度准确的长读测序（PacBio HiFi）来表征拟南芥msh1突变个体的线粒体和质体基因组变异。HiFi读数提供了重组动力学的全局视图，详细定量了大重复和小重复的亲本和交叉重组产物。我们发现，重组断点分布相对均匀的重复序列的长度和检测到广泛的内部交换的序列变异对不完美的重复msh1突变体的线粒体基因组。从其他7个拟南芥野生型加入的线粒体基因组的长读组件不同的重复介导的结构重排类似于在msh1突变体中观察到的，但他们都在一个简单的低异质性状态。拟南芥质体基因组一般缺乏小重复序列，并表现出非常不同的模式的变体积累msh1突变体相比，线粒体基因组。我们的数据说明了HiFi技术在研究植物细胞器基因组中重复介导的重组中的作用，并提高了MSH1抑制的重组过程的序列分辨率。植物细胞器基因组可以经历快速重排。长读测序提供了一个详细的和定量的线粒体和质体基因组变异通常抑制MSH1，推进我们对植物细胞器基因组动态的理解。
The abundant repeats in plant mitochondrial genomes can cause rapid genome rearrangements and are also a major obstacle in short-read sequencing studies. Nuclear-encoded proteins such as MSH1 are known to suppress the generation of repeat-associated mitochondrial genome variants, but our understanding of these mechanisms has been constrained by the limitations of short-read technologies. Here, we used highly accurate long-read sequencing (PacBio HiFi) to characterize mitochondrial and plastid genome variants in Arabidopsis thaliana msh1 mutant individuals. The HiFi reads provided a global view of recombination dynamics with detailed quantification of parental and crossover recombination products for both large and small repeats. We found that recombination breakpoints were distributed relatively evenly across the length of repeated sequences and detected widespread internal exchanges of sequence variants between pairs of imperfect repeats in the mitochondrial genome of msh1 mutants. Long-read assemblies of mitochondrial genomes from seven other Arabidopsis thaliana wild-type accessions differed by repeat-mediated structural rearrangements similar to those observed in msh1 mutants, but they were all in a simple low-heteroplasmy state. The Arabidopsis plastid genome generally lacks small repeats and exhibited a very different pattern of variant accumulation in msh1 mutants compared with the mitochondrial genome. Our data illustrate the power of HiFi technology in studying repeat-mediated recombination in plant organellar genomes and improved the sequence resolution for recombinational processes suppressed by MSH1. Plant organellar genomes can undergo rapid rearrangements. Long-read sequencing provides a detailed and quantitative view of mitochondrial and plastid genome variants normally suppressed by MSH1, advancing our understanding of plant organellar genome dynamics.
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影响因子：
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作者：
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DOI：
10.15252/embj.2020104858
发表时间：
2020-11-02
期刊：
The EMBO journal
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