Mitochondrial genome (mtDNA) carries not only well-conserved protein coding, tRNA and rRNA genes, but also highly variable non-coding regions (NCRs). However, the NCRs show poor conservation across species, making their function and evolution elusive. Identification and functional characterization of NCRs across species would be critical for addressing these questions. To this end, we devised a computational pipeline and performed de novo assembly and annotation of mtDNA from 19 Caenorhabditis species using next-generation sequencing (NGS) data. The mtDNAs for 14 out of the 19 species are reported for the first time. Comparison of the 19 genomes reveals species-specific sampling of partial displacement-loop (D-loop) sequence as a novel NCR inserted into a unique tRNA cluster, suggesting an important role of the D-loop and the tRNA cluster in shaping NCR evolution. Intriguingly, RNA-Seq analysis suggests that a novel NCR resulting from a recent duplication of NADH dehydrogenase subunit 5 (ND5) could be utilized as a 3' UTR for up-regulation of its upstream gene. The expression analysis shows a species- and sex-specific expression of mitochondrial genes encoded by mtDNA and nucleus, respectively. Our analyses provide important insights into the function and evolution of mitochondrial NCRs and pave the way for further studying the function and evolution of mitochondrial genome.

中文翻译：

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比较线粒体基因组学揭示了近期 NADH 脱氢酶亚基 5 重复在基因调控中的可能作用。

线粒体基因组 (mtDNA) 不仅携带高度保守的蛋白质编码、tRNA 和 rRNA 基因，还携带高度可变的非编码区 (NCR)。然而，NCR 在不同物种之间表现出较差的保护性，使得它们的功能和进化难以捉摸。跨物种 NCR 的识别和功能表征对于解决这些问题至关重要。为此，我们设计了一个计算流程，并使用下一代测序 (NGS) 数据对 19 种秀丽隐杆线虫物种的 mtDNA 进行从头组装和注释。19个物种中有14个的mtDNA是首次报道。19 个基因组的比较揭示了部分置换环 (D-loop) 序列的物种特异性采样，作为插入独特 tRNA 簇的新型 NCR，表明 D-环和 tRNA 簇在塑造 NCR 进化中的重要作用。有趣的是，RNA-Seq 分析表明，由 NADH 脱氢酶亚基 5 (ND5) 最近重复产生的新型 NCR 可以用作 3' UTR，上调其上游基因。表达分析显示了分别由 mtDNA 和细胞核编码的线粒体基因的物种特异性和性别特异性表达。我们的分析为线粒体NCR的功能和进化提供了重要的见解，并为进一步研究线粒体基因组的功能和进化铺平了道路。