The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana
The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana
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DOI：
10.1534/g3.119.401023
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发表时间：
2019-09
期刊：
影响因子：
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通讯作者：
Zhiqiang Wu;Gus Waneka;Daniel B. Sloan
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文献类型：
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作者：
Zhiqiang Wu;Gus Waneka;Daniel B. Sloan
被子植物线粒体基因组序列差异的机制一直是个谜。特别是，它是很难调和的基因间区域的快速分歧，可以使非编码序列几乎无法识别，甚至在近亲与基因区域中发现的序列保守性异常高的水平。有人假设不同的突变和修复机制作用于基因和基因间序列，或者突变输入相对恒定，但选择对这些相应区域具有显著不同的影响。为了测试这些替代的可能性，我们分析了拟南芥中的mtDNA差异，包括来自1001基因组计划的变体和已发表的突变积累（MA）系中的变化。我们发现，碱基置换频率是相对相似的基因间区域和同义位点的编码区，而插入缺失和非同义置换率大大压抑在编码区，支持一个传统的模型，其中突变/修复机制是一致的整个基因组，但差异过滤选择。大多数类型的序列和结构的变化是无法检测到的10代MA线，但我们发现显着的变化，在整个mtDNA区域的相对拷贝数在压力与良性条件下生长的线。我们证实了A.我们使用全基因组测序和液滴数字PCR技术对拟南芥线粒体基因组进行了测序，进一步破坏了经典但过于简化的圆形被子植物mtDNA结构模型。我们的研究结果表明，拷贝数变异是被子植物线粒体基因组最具流动性的特征之一。
The mechanisms of sequence divergence in angiosperm mitochondrial genomes have long been enigmatic. In particular, it is difficult to reconcile the rapid divergence of intergenic regions that can make non-coding sequences almost unrecognizable even among close relatives with the unusually high levels of sequence conservation found in genic regions. It has been hypothesized that different mutation and repair mechanisms act on genic and intergenic sequences or alternatively that mutational input is relatively constant but that selection has strikingly different effects on these respective regions. To test these alternative possibilities, we analyzed mtDNA divergence within Arabidopsis thaliana, including variants from the 1001 Genomes Project and changes accrued in published mutation accumulation (MA) lines. We found that base-substitution frequencies are relatively similar for intergenic regions and synonymous sites in coding regions, whereas indel and nonsynonymous substitutions rates are greatly depressed in coding regions, supporting a conventional model in which mutation/repair mechanisms are consistent throughout the genome but differentially filtered by selection. Most types of sequence and structural changes were undetectable in 10-generation MA lines, but we found significant shifts in relative copy number across mtDNA regions for lines grown under stressed vs. benign conditions. We confirmed quantitative variation in copy number across the A. thaliana mitogenome using both whole-genome sequencing and droplet digital PCR, further undermining the classic but oversimplified model of a circular angiosperm mtDNA structure. Our results suggest that copy number variation is one of the most fluid features of angiosperm mitochondrial genomes.