Department of Biology, Colorado State University.
Genome Biol Evol. 2013;5(9):1652-60. doi: 10.1093/gbe/evt119.
Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.
线粒体是细胞内的细胞器，在这里进行氧化磷酸化以完成 ATP 合成。线粒体有自己的基因组；在后生动物中，这是一个小的、圆形的分子，编码 13 种电子传递蛋白、22 种 tRNA 和 2 种 rRNA。在无脊椎动物中，线粒体基因重排很常见，并且与替代率的增加有关。在脊椎动物中，线粒体基因重排很少见，其与替代率的关系仍未得到探索。线粒体基因也可以由于 mtDNA 复制的机制而在基因组周围表现出替代率的空间变化，该机制产生了一个突变梯度。然而，迄今为止，突变梯度的强度以及在重排（或其他修饰）基因组中沿着梯度的运动是否会影响基因的替代率，在大多数脊椎动物中仍未得到探索。蝾螈包括正常的线粒体基因组和独立衍生的重排和扩张，为测试基因组结构的大规模变化对脊椎动物线粒体基因序列进化的影响提供了难得的机会。我们表明：1）重排/扩张的基因组具有更高的替代率；2）重排/扩张基因组中的大多数基因都沿着突变梯度保持其位置，替代率发生移动的基因不受其新位置的影响，并且蝾螈的梯度较弱；3）基因组重排/扩张与基因的选择约束水平无关。总之，我们的结果表明，基因组结构的大规模变化以可预测的方式影响线粒体基因的进化；然而，尽管存在这些影响，但相同的功能约束作用于修饰和正常基因组中的线粒体蛋白编码基因。
