Department of Biology, University of Bari, Bari, 70124, Italy.
School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
Sci Rep. 2017 Nov 27;7(1):16357. doi: 10.1038/s41598-017-16750-2.
The colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays an important role in genomic variability. Notwithstanding the DNA sequence availability of about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number of sequenced eukaryotic species. With the aim to clarify the time and way of NumtS evolution, we explored the genomic distribution of NumtS in 23 eukaryotic species using an intra/interspecies in silico approach based on a cross-species similarity search and deeply investigate the evolution of NumtS in mammals. The intra- and interspecies analysis underlined how some mitochondrial regions that populated nuclear genomes can be considered as hotspots. Considering the large amount of NumtS we found in platypus and opossum genomes, we hypothesized the occurrence of an earlier colonization that happened prior to the Prototherian/Therian mammal divergence, approximately 160-210 million years ago. These events are still detectable due to the species-specific dynamics that have affected these genomes. Phylogenetic analyses of NumtS derived from two different mitochondrial DNA loci allowed us to recognize the unusual NumtS evolution that acted differently on primate and non-primate species' genomes.
线粒体 DNA 对核基因组的殖民是真核生物中一个持续的过程，在基因组变异性中起着重要作用。尽管大约 100 个完整真核基因组的 DNA 序列已经可用，但迄今为止，NumtS 的分布仅在少数测序真核物种中得到了全面报道。为了阐明 NumtS 的进化时间和方式，我们使用基于跨物种相似性搜索的种内/种间计算机模拟方法，探索了 23 种真核生物物种中 NumtS 的基因组分布，并深入研究了哺乳动物中 NumtS 的进化。种内和种间分析强调了一些填充核基因组的线粒体区域如何可以被视为热点。考虑到我们在鸭嘴兽和负鼠基因组中发现的大量 NumtS，我们假设发生了一次更早的殖民，发生在原兽亚纲/真兽亚纲哺乳动物分化之前，大约在 1.6 亿到 2.1 亿年前。由于这些基因组受到了物种特异性动态的影响，这些事件仍然可以检测到。从两个不同的线粒体 DNA 基因座得出的 NumtS 的系统发育分析使我们能够识别出在灵长类和非灵长类物种基因组上表现不同的异常 NumtS 进化。
