Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany.
School of Life Science, University of Sussex, Brighton BN1 9QG, UK.
Genome Biol Evol. 2022 Jul 2;14(7). doi: 10.1093/gbe/evac104.
Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
线粒体基因的核拷贝（numts）在脊椎动物基因组中很常见，在许多物种中都有特征描述。然而，人们相对较少关注理解它们的进化起源以及厘清插入的替代来源。包含具有完整线粒体阅读框的基因的 numts 是为此目的的良好候选物。它们所包含的基因序列可以与其线粒体同源物进行比较，以描述同义到非同义替换率，这可以揭示这些基因所经历的选择压力。在这里，我们描述了南极毛皮海豹（Arctocephalus gazella）基因组中的 25 个 numts。在那些包含具有完整线粒体阅读框的基因的 numts 中，有三个与它们的线粒体同源物相比有多个替换。我们的分析表明，其中一个代表了一个历史上的插入物，自从它在富含逆转录转座子的基因组区域中殖民到Otarioidea 以来，一直受到强烈的纯化选择。相比之下，另外两个 numts 似乎是更近的，它们大量的替换可以归因于非规范的插入，要么是异质 mtDNA 的整合，要么是杂交。我们的研究揭示了鳍足类 numts 的进化历史，并揭示了隐藏的线粒体核变异来源的存在。
