Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological and Environment, Wuhan 430010, Hubei, China.
Eco-Environmental Monitoring Station of Pu'er City, Yunnan Provincial Department of Ecology and Environment, Pu'er 665000, Yunnan, China.
Gene. 2024 Jan 20;892:147847. doi: 10.1016/j.gene.2023.147847. Epub 2023 Sep 28.
Acorus tatarinowii Schott (A. tatarinowii), a well-known traditional Chinese medicinal plant renowned for its high medicinal value, but its mitochondrial genome (mitogenome) is still unexplored. In this study, we meticulously assembled the complete mitochondrial genome of A. tatarinowii using a combination of Illumina short reads and Oxford Nanopore long reads. Our findings revealed that A. tatarinowii possesses a complex chromosomal structural mitogenome, comprising two linear chromosomes and seven circular chromosomes. This mitogenome spans 1.81 Mb in length with a GC content of 38.29 %. Notably, it contained 24 unique mitochondrial core genes, seven unique variable genes, 17 tRNA genes, and three rRNA genes. Analyses of codon usage, most protein-coding genes (PCGs) exhibited a common codon usage preference, with RSCU values greater than 1, and the codon with the highest RSCU value was UAA(End, 1.90). We conducted a thorough analysis of repeat sequences, the distribution of repetitive sequences in nine mitochondrial chromosomes showed distinct patterns. Moreover, we identified 82 and 12 homologous fragments by comparing the sequences of chloroplast and nuclear genomes to the A. tatarinowii mitogenome, respectively. Lastly, We predicted a total of 234 potential RNA editing sites in 28 unique PCGs and discovered that the nad4 gene has been edited the most often, at 26 times. Our results contribute to the enrichment of mitochondrial genome resources for Acoraceae, and the mitogenome also can be used as a reference for other species.
石菖蒲（Acorus tatarinowii）是一种著名的传统中药材，具有很高的药用价值，但它的线粒体基因组（mitogenome）尚未被研究过。在这项研究中，我们使用 Illumina 短读和 Oxford Nanopore 长读相结合的方法，精心组装了 A. tatarinowii 的完整线粒体基因组。我们的研究结果表明，A. tatarinowii 拥有复杂的染色体结构线粒体基因组，由两条线性染色体和七条圆形染色体组成。这个线粒体基因组长 1.81 Mb，GC 含量为 38.29%。值得注意的是，它包含 24 个独特的线粒体核心基因、7 个独特的可变基因、17 个 tRNA 基因和 3 个 rRNA 基因。对密码子使用的分析表明，大多数蛋白质编码基因（PCGs）表现出共同的密码子使用偏好，RSCU 值大于 1，RSCU 值最高的密码子是 UAA（终止密码子，1.90）。我们对重复序列进行了深入分析，发现九个线粒体染色体中重复序列的分布存在明显的模式。此外，我们通过比较叶绿体和核基因组与 A. tatarinowii 线粒体基因组的序列，分别鉴定了 82 个和 12 个同源片段。最后，我们在 28 个独特的 PCGs 中预测了总共 234 个潜在的 RNA 编辑位点，并发现 nad4 基因的编辑次数最多，达到 26 次。我们的研究结果丰富了 Acoraceae 线粒体基因组资源，该线粒体基因组也可作为其他物种的参考。
