Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates
Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates
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DOI：
10.1093/genetics/iyab039
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发表时间：
2021-03-11
期刊：
影响因子：
3.3
通讯作者：
Sloan, Daniel B.
中科院分区：
文献类型：
--
作者：
Broz, Amanda K.;Waneka, Gus;Sloan, Daniel B.
虽然植物线粒体基因组通常表现出较低的序列进化率，但某些被子植物谱系中的分歧水平表明线粒体突变率非常高。然而，从未在此类谱系中直接分析过从头突变。高保真DNA测序技术的最新进展使得能够在仍以低异质频率存在时检测线粒体突变。迄今为止，这些方法仅在单一植物物种（拟南芥）上进行。在这里，我们应用高保真技术（双链测序）的多个被子植物属蝇子草，表现出极大的异质性，在近亲之间的线粒体序列进化的速度。与系统发育的证据相一致，我们发现，宽叶蝇子草保持较低的线粒体变异频率，与以前的测量在拟南芥。尽管历史序列差异很高，但黄花蝇子草也表现出较低的变异频率，这支持了其他证据，即该物种在过去的加速事件后恢复到较低的线粒体突变率。与此相反，S.圆锥形在线粒体DNA中显示出更高的变异频率（但不在质体中），这与正在进行的线粒体突变率升高相一致。此外，我们发现了一个改变的突变谱在S。conica严重偏向AT -> GC转换。我们还观察到在S.圆锥，潜在地指向同源重组的机会减少，以准确地修复该物种中的错配。总体而言，这些结果表明，突变率的历史波动正在推动植物线粒体序列进化速率的极端变化。
Although plant mitochondrial genomes typically show low rates of sequence evolution, levels of divergence in certain angiosperm lineages suggest anomalously high mitochondrial mutation rates. However, de novo mutations have never been directly analyzed in such lineages. Recent advances in high-fidelity DNA sequencing technologies have enabled detection of mitochondrial mutations when still present at low heteroplasmic frequencies. To date, these approaches have only been performed on a single plant species (Arabidopsis thaliana). Here, we apply a high-fidelity technique (Duplex Sequencing) to multiple angiosperms from the genus Silene, which exhibits extreme heterogeneity in rates of mitochondrial sequence evolution among close relatives. Consistent with phylogenetic evidence, we found that Silene latifolia maintains low mitochondrial variant frequencies that are comparable with previous measurements in Arabidopsis. Silene noctiflora also exhibited low variant frequencies despite high levels of historical sequence divergence, which supports other lines of evidence that this species has reverted to lower mitochondrial mutation rates after a past episode of acceleration. In contrast, S. conica showed much higher variant frequencies in mitochondrial (but not in plastid) DNA, consistent with an ongoing bout of elevated mitochondrial mutation rates. Moreover, we found an altered mutational spectrum in S. conica heavily biased towards AT -> GC transitions. We also observed an unusually low number of mitochondrial genome copies per cell in S. conica, potentially pointing to reduced opportunities for homologous recombination to accurately repair mismatches in this species. Overall, these results suggest that historical fluctuations in mutation rates are driving extreme variation in rates of plant mitochondrial sequence evolution.