Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.

中文翻译：

---

草莓有丝分裂基因组在结构上快速进化，但在序列上缓慢进化，并导致由微倒位介导的频繁多核苷酸突变。

植物线粒体 DNA 被描述为在结构上快速进化，但在序列上缓慢进化。然而，植物有丝分裂基因组的许多非编码部分在物种之间不是同源的，这引发了关于非编码区突变率和谱的问题。最近的研究表明，非编码区缺乏同源性可能是由于序列差异增加。我们比较了来自 13 个已测序的草莓有丝分裂基因组的 30 kb 编码 DNA 和 200 kb 非编码 DNA，然后分析了序列发散率、微倒位事件和结构变异。同义位点和非基因位点的替换率几乎相同，表明全基因组点突变率基本一致。在草莓有丝分裂基因组中检测到数量惊人的大多核苷酸取代，这可能是由微倒位事件引起的，并可能影响系统发育信号和局部速率估计。相对于插入和大量基因组排列，草莓有丝分裂基因组优先积累缺失，而突变率可能与物种间的这些序列和结构变化正相关。总之，这些观察结果表明植物有丝分裂基因组在全基因组范围内表现出低点突变，但结构变异异常高，我们的结果有利于植物有丝分裂基因组之间同源性快速丧失的增益和损失模型。相对于插入和大量基因组排列，草莓有丝分裂基因组优先积累缺失，而突变率可能与物种间的这些序列和结构变化正相关。总之，这些观察结果表明植物有丝分裂基因组在全基因组范围内表现出低点突变，但结构变异异常高，我们的结果有利于植物有丝分裂基因组之间同源性快速丧失的增益和损失模型。相对于插入和大量基因组排列，草莓有丝分裂基因组优先积累缺失，而突变率可能与物种间的这些序列和结构变化正相关。总之，这些观察结果表明植物有丝分裂基因组在全基因组范围内表现出低点突变，但结构变异异常高，我们的结果有利于植物有丝分裂基因组之间同源性快速丧失的增益和损失模型。