Shao Renfu, Barker Stephen C, Mitani Harumi, Aoki Yayoi, Fukunaga Masahito
Department of Microbiology and Parasitology, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
Mol Biol Evol. 2005 Mar;22(3):620-9. doi: 10.1093/molbev/msi047. Epub 2004 Nov 10.
To investigate the evolution pattern and phylogenetic utility of duplicate control regions (CRs) in mitochondrial (mt) genomes, we sequenced the entire mt genomes of three Ixodes species and part of the mt genomes of another 11 species. All the species from the Australasian lineage have duplicate CRs, whereas the other species have one CR. Sequence analyses indicate that the two CRs of the Australasian Ixodes ticks have evolved in concert in each species. In addition to the Australasian Ixodes ticks, species from seven other lineages of metazoa also have mt genomes with duplicate CRs. Accumulated mtDNA sequence data from these metazoans and two recent experiments on replication of mt genomes in human cell lines with duplicate CRs allowed us to re-examine four intriguing questions about the presence of duplicate CRs in the mt genomes of metazoa: (1) Why do some mt genomes, but not others, have duplicate CRs? (2) How did mt genomes with duplicate CRs evolve? (3) How could the nucleotide sequences of duplicate CRs remain identical or very similar over evolutionary time? (4) Are duplicate CRs phylogenetic markers? It appears that mt genomes with duplicate CRs have a selective advantage in replication over mt genomes with one CR. Tandem duplication followed by deletion of genes is the most plausible mechanism for the generation of mt genomes with duplicate CRs. Once duplicate CRs occur in an mt genome, they tend to evolve in concert, probably by gene conversion. However, there are lineages where gene conversion may not always occur, and, thus, the two CRs may evolve independently in these lineages. Duplicate CRs have much potential as phylogenetic markers at low taxonomic levels, such as within genera, within families, or among families, but not at high taxonomic levels, such as among orders.
为了研究线粒体（mt）基因组中重复控制区（CRs）的进化模式及其系统发育效用，我们对三种硬蜱属物种的完整mt基因组以及另外11种物种的部分mt基因组进行了测序。所有澳大拉西亚谱系的物种都有重复的CRs，而其他物种只有一个CR。序列分析表明，澳大拉西亚硬蜱属蜱虫的两个CRs在每个物种中都是协同进化的。除了澳大拉西亚硬蜱属蜱虫外，后生动物其他七个谱系的物种也有含有重复CRs的mt基因组。来自这些后生动物积累的mtDNA序列数据以及最近两项关于在具有重复CRs的人类细胞系中mt基因组复制的实验，使我们能够重新审视关于后生动物mt基因组中存在重复CRs的四个有趣问题：（1）为什么有些mt基因组有重复的CRs，而有些没有？（2）含有重复CRs的mt基因组是如何进化的？（3）在进化过程中，重复CRs的核苷酸序列如何保持相同或非常相似？（4）重复CRs是系统发育标记吗？似乎含有重复CRs的mt基因组在复制方面比只有一个CR的mt基因组具有选择优势。串联重复随后基因缺失是产生含有重复CRs的mt基因组最合理的机制。一旦mt基因组中出现重复CRs，它们往往会协同进化，可能是通过基因转换。然而，有些谱系中基因转换可能并不总是发生，因此，这两个CRs在这些谱系中可能会独立进化。重复CRs在低分类水平，如属内、科内或科间，作为系统发育标记有很大潜力，但在高分类水平，如目间则不然。
