Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants
Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants
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DOI：
10.1093/molbev/msp249
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发表时间：
2010-02-01
影响因子：
10.7
通讯作者：
Gaut, Brandon S.
中科院分区：
文献类型：
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作者：
Hollister, Jesse D.;Ross-Ibarra, Jeffrey;Gaut, Brandon S.
最近提出的突变机制，插入/缺失相关突变（IDAM），假定杂合插入/缺失（插入/缺失）增加附近的核苷酸的点突变率由于减数分裂期间的错误。这种机制可能对植物基因组的进化具有特别动态的后果，因为植物物种之间自花受精率的高度变化导致等位基因（包括插入缺失等位基因）的杂合性在植物物种中分离的差异。在这项研究中，我们调查了IDAM的后果，在交配系统不同的物种使用正向群体遗传模拟和全基因组DNA重测序数据从拟南芥，水稻，普通野生稻。不同水平的自交模拟表明，IDAM对周围的核苷酸多样性的影响应减少增加自交率。结合自交率和自交开始时间的进一步模拟表明，自切换到自交以来的时间也会影响IDAM导致的核苷酸多样性模式。群体遗传学分析表明，A. thaliana和Oryza的DNA序列数据集经验性地证实了我们的模拟结果，揭示了IDAM在异交O. rufipogon，在最近进化的selfer O. sativa，而相对古老的自交系A. thaliana.这些结果支持了一个新的观点，即生活史的差异，如自交水平，可以影响物种之间的个体突变率。
A recently proposed mutational mechanism, indel-associated mutation (IDAM), posits that heterozygous insertions/deletions (indels) increase the point mutation rate at nearby nucleotides due to errors during meiosis. This mechanism could have especially dynamic consequences for the evolution of plant genomes, because the high degree of variation in the rate of self-fertilization among plant species causes differences in the heterozygosity of alleles, including indel alleles, segregating in plant species. In this study, we investigated the consequences of IDAM for species differing in mating system using both forward population genetic simulations and genomewide DNA resequencing data from Arabidopsis thaliana, Oryza sativa, and Oryza rufipogon. Simulations of different levels of selfing suggest that the effect of IDAM on surrounding nucleotide diversity should decrease with increasing selfing rate. Further simulations incorporating selfing rates and the time of onset of selfing suggest that the time since the switch to selfing also affects patterns of nucleotide diversity due to IDAM. Population genetic analyses of A. thaliana and Oryza DNA sequence data sets empirically confirmed our simulation results, revealing the strongest effect of IDAM in the outcrossing O. rufipogon, a weaker effect in the recently evolved selfer O. sativa, and the weakest effect in the relatively ancient selfer A. thaliana. These results support the novel idea that differences in life history, such as the level of selfing, can affect the per-individual mutation rate among species.