Luo Xianyang, Gu Cuicui, Gao Sijia, Li Man, Zhang Haixiang, Zhu Shidong
College of Horticulture, Anhui Agricultural University, Hefei, China.
Front Plant Sci. 2024 Aug 9;15:1381089. doi: 10.3389/fpls.2024.1381089. eCollection 2024.
(Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of , respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of , accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of . Also, approximately 85% of fragments from the mitogenome were duplicated in the nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for , , , , and . A total of 93 RNA editing sites were found in the PCGs of the mitogenome. and are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of .
(Griseb.) Turcz. ex Stapf因其重要的营养、药用、生态和经济价值，在中国已被培育成为一种受欢迎的水生蔬菜。此前尚未对其完整的线粒体基因组（mitogenome）进行研究和报道，这阻碍了其分子系统学研究以及对进化过程的理解。在此，我们组装了该物种的完整线粒体基因组，并进行了全面分析，包括基因组组织、重复序列、RNA编辑事件、细胞间基因转移、系统发育分析和比较线粒体基因组分析。该物种的线粒体基因组估计为一个392,219 bp的环状分子，包含58个基因，由3个rRNA基因、20个tRNA基因和35个蛋白质编码基因（PCGs）组成。分别从该物种的线粒体基因组和叶绿体基因组中鉴定出46个和20个具有不同基序的简单序列重复（SSRs）。此外，观察到49个同源片段从叶绿体基因组转移到该物种的线粒体基因组，占整个线粒体基因组的47,500 bp，占比12.1%。另外，该物种的线粒体基因组和叶绿体基因组之间存在11个含基因的同源区域。而且，线粒体基因组中约85%的片段在该物种的核基因组中重复。选择压力分析表明，除了[具体基因名称1]、[具体基因名称2]、[具体基因名称3]、[具体基因名称4]和[具体基因名称5]外，大多数线粒体基因高度保守。在线粒体基因组的PCGs中总共发现了93个RNA编辑位点。共线性分析和系统发育分析表明，[具体物种1]和[具体物种2]关系最为密切。我们发现稻亚科植物线粒体基因组中的重复序列和外源序列与基因组重排有关。总体而言，该物种线粒体基因组的可得性将为我们理解该物种的分子和基因组方面提供有价值的信息。
