Université Paris-Saclay, INRAE, AgroParisTech, GABI, F-78350, Jouy-en-Josas, France.
INRAE, SIGENAE, F-78350, Jouy-en-Josas, France.
Sci Rep. 2020 Feb 7;10(1):2077. doi: 10.1038/s41598-020-59155-4.
Nuclear copies of the mitochondrial DNA (NUMTs) have already been described in several species. In this context, we identified and analysed 166 bovine NUMT regions with a total length of 430 kbp, representing about 0.02% of the cattle nuclear genome. Copies of all mitochondrial regions were detected in the nuclear genome, with distinct degrees of sequence similarity to the mitogenome. Some NUMT regions include large mitogenome segments and show high similarity to the organelle genome sequence. NUMT regions are frequently modified by insertion of repetitive sequences and by sequence rearrangements. We confirmed the existence of 29 NUMT regions by PCR amplification using DNA from the cow (Dominette) which was used to generate the bovine genome reference sequence, ruling out the possibility that these NUMTs could be artifacts of the genome assembly. As there are NUMT regions with high similarity to the mitogenome, special care is needed when designing primers for mitochondrial DNA amplification. Our results can therefore be used to avoid co-amplification of bovine nuclear sequences similar to mitochondrial DNA.
线粒体 DNA（NUMTs）的核拷贝已在多种物种中被描述。在此背景下，我们鉴定和分析了 166 个牛 NUMT 区域，总长 430 kbp，占牛核基因组的约 0.02%。所有线粒体区域的拷贝都在核基因组中被检测到，与线粒体基因组具有不同程度的序列相似性。一些 NUMT 区域包含大片段的线粒体基因组，并且与细胞器基因组序列高度相似。NUMT 区域经常通过插入重复序列和序列重排而发生修饰。我们通过使用来自用于生成牛基因组参考序列的奶牛（Dominette）的 DNA 进行 PCR 扩增，证实了 29 个 NUMT 区域的存在，排除了这些 NUMTs 可能是基因组组装的人工制品的可能性。由于存在与线粒体基因组高度相似的 NUMT 区域，因此在设计用于扩增线粒体 DNA 的引物时需要特别小心。因此，我们的结果可用于避免类似线粒体 DNA 的牛核序列的共扩增。
