Plant Organelle Genome Research Center, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan.
Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan.
Mitochondrion. 2019 May;46:179-186. doi: 10.1016/j.mito.2018.05.001. Epub 2018 Jul 10.
The structures of plant mitochondrial genomes are more complex than those of animals. One of the reasons for this is that plant mitochondrial genomes typically have many long and short repeated sequences and intra- and intermolecular recombination may create various DNA molecules in this organelle. Recombination may sometimes create a novel gene that causes cytoplasmic male sterility (CMS). The onion has several cytoplasm types, with some causing CMS while others do not. The complete mitochondrial genome sequence of the onion was reported for an inbred line with CMS-S cytoplasm; however, the number of differences between onion strains remains unclear, and studies on purified mitochondrial DNA (mtDNA) have not yet been performed. Furthermore, analyses of transcripts in the mitochondrial genome have not been conducted. In the present study, we examined the mitochondrial genome of the onion variety "Momiji-3" (Allium cepa L.) possessing CMS-S-type cytoplasm using next-generation sequencing (NGS). The "Momiji-3" mitochondrial genome mainly exists as three circles as a result of recombination through repeated sequences and we herein succeeded for the first time in visualizing its structure using pulsed field gel electrophoresis (PFGE). The ability to clarify the structure of the mitochondrial genome is rare in plant mitochondria; therefore, "Momiji-3" represents a good example for elucidating complex plant mitochondrial genomes. We also mapped transcript data to the mitochondrial genome in order to identify the RNA-editing positions in all gene-coding regions and estimate the expression levels of genes. We identified 635 editing positions in gene-coding regions. Start and stop codons were created by RNA editing in six genes (nad1, nad4L, atp6, atp9, ccmFC, and orf725). The transcript amounts of novel open reading frames (ORFs) were all markedly lower than those of functional genes. These results suggest that a new functional gene was not present in the mitochondrial genome of "Momiji-3", and that the candidate gene for CMS is orf725, as previously reported.
植物线粒体基因组的结构比动物的更复杂。造成这种情况的原因之一是，植物线粒体基因组通常具有许多长的和短的重复序列，并且内和分子间重组可能会在这个细胞器中产生各种 DNA 分子。重组有时会产生一个新的基因，导致细胞质雄性不育（CMS）。洋葱有几种细胞质类型，其中一些导致 CMS，而另一些则不导致 CMS。具有 CMS-S 细胞质的洋葱近交系的完整线粒体基因组序列已经被报道；然而，洋葱株系之间的差异数量尚不清楚，并且尚未对纯化的线粒体 DNA（mtDNA）进行研究。此外，对线粒体基因组中转录物的分析尚未进行。在本研究中，我们使用下一代测序（NGS）检查了具有 CMS-S 型细胞质的洋葱品种“Momiji-3”（Allium cepa L.）的线粒体基因组。“Momiji-3”线粒体基因组主要以三个环的形式存在，这是由于通过重复序列进行重组的结果，我们首次成功地使用脉冲场凝胶电泳（PFGE）可视化其结构。阐明线粒体基因组结构的能力在植物线粒体中很少见；因此，“Momiji-3”为阐明复杂的植物线粒体基因组提供了一个很好的范例。我们还将转录数据映射到线粒体基因组上，以确定所有基因编码区的 RNA 编辑位置并估计基因的表达水平。我们在基因编码区鉴定了 635 个编辑位置。在六个基因（nad1、nad4L、atp6、atp9、ccmFC 和 orf725）中，RNA 编辑产生了起始和终止密码子。新开放阅读框（ORF）的转录物量均明显低于功能基因。这些结果表明，“Momiji-3”的线粒体基因组中没有新的功能基因，并且候选 CMS 基因是 orf725，如前所述。
