Faculty of Life Science, Kyoto Sangyo University, Kyoto, Kyoto, Japan.
Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Sci Rep. 2019 Feb 14;9(1):2060. doi: 10.1038/s41598-019-38607-6.
Nuclear genomes are always faced with the modification of themselves by insertions and integrations of foreign DNAs and intrinsic parasites such as transposable elements. There is also substantial number of integrations from symbiotic organellar genomes to their host nuclear genomes. Such integration might have acted as a beneficial mutation during the evolution of symbiosis, while most of them have more or less deleterious effects on the stability of current genomes. Here we report the pattern of DNA substitution and methylation on organellar DNA fragments integrated from plastid into plant nuclear genomes. The genome analyses of 17 plants show homology-dependent DNA substitution bias. A certain number of these sequences are DNA methylated in the nuclear genome. The intensity of DNA methylation also decays according to the increase of relative evolutionary times after being integrated into nuclear genomes. The methylome data of epigenetic mutants shows that the DNA methylation of organellar DNA fragments in nuclear genomes are mainly dependent on the methylation maintenance machinery, while other mechanisms may also affect on the DNA methylation level. The DNA methylation on organellar DNA fragments may contribute to maintaining the genome stability and evolutionary dynamics of symbiotic organellar and their host's genomes.
核基因组总是面临着自身被插入和整合外源 DNA 和内源性寄生虫（如转座元件）的修饰。还有大量来自共生细胞器基因组到其宿主核基因组的整合。这种整合在共生进化过程中可能起到了有益突变的作用，而大多数整合对当前基因组的稳定性或多或少都有不利影响。在这里，我们报告了从质体整合到植物核基因组的细胞器 DNA 片段的 DNA 取代和甲基化模式。对 17 种植物的基因组分析显示，同源依赖性 DNA 取代偏倚。这些序列中有一定数量在核基因组中发生 DNA 甲基化。这些序列在整合到核基因组后，根据相对进化时间的增加，其 DNA 甲基化强度也会衰减。表观遗传突变体的甲基组数据表明，核基因组中细胞器 DNA 片段的 DNA 甲基化主要依赖于甲基化维持机制，而其他机制也可能影响 DNA 甲基化水平。细胞器 DNA 片段的 DNA 甲基化可能有助于维持共生细胞器及其宿主基因组的基因组稳定性和进化动态。
