Omelchenko Denis O, Makarenko Maxim S, Kasianov Artem S, Schelkunov Mikhail I, Logacheva Maria D, Penin Aleksey A
Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia.
Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
Plants (Basel). 2020 Apr 8;9(4):469. doi: 10.3390/plants9040469.
Shepherd's purse () is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of differs from , but not from , by two long inversions, suggesting that could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except and contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in .
荠菜（）是一种分布于世界各地的一年生杂草，也是研究被子植物进化中异源多倍体化的一种很有前景的模式植物。虽然植物线粒体基因组是遗传信息的宝贵来源，但它们很难组装。目前，在荠菜属的所有物种中，只有荠菜的完整线粒体基因组可用。在这项工作中，我们使用高精度的PacBio SMRT第三代测序技术组装了荠菜的完整线粒体基因组。它长287,799 bp，包含32个蛋白质编码基因、3个rRNA、25个对应15种氨基酸的tRNA以及8个由RNAseq数据支持的开放阅读框（ORF）。虽然发现了许多重复区域，但它们都不超过1 kbp，并且这些重复产生的最常见结构变异仅存在于4%的线粒体基因组拷贝中。荠菜的线粒体DNA序列与荠菜不同，但与荠菜不同之处在于有两个长倒位，这表明荠菜可能是其母本祖先物种。总共检测到377个C到U的RNA编辑位点。除了和之外，所有基因都含有RNA编辑位点，并且它们中的大多数导致氨基酸的非同义变化。大多数已鉴定的RNA编辑位点与荠菜中的相应RNA编辑位点相同。
