Wang Yuliang, Li Qiang, Jian Xing
College of Biomedicine and Health, Anhui Science and Technology University, Fengyang, 233100, China.
College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
Genetica. 2025 Jul 16;153(1):25. doi: 10.1007/s10709-025-00241-8.
Phyllanthus fluitans, a member of the Phyllanthaceae, is a unique free-floating aquatic species exhibiting considerable ornamental value. In this study, we assembled the mitochondrial genome of P. fluitans representing the first mitochondrial genome report of the Phyllanthaceae family. The mitogenome comprises two circular chromosomes spanning 230,785 bp (chromosome 1) and 143,421 bp (chromosome 2), collectively harboring 32 protein-coding genes (PCGs), 25 tRNA genes, four rRNA genes, and one pseudogene. Structural analyses identified 118 simple sequence repeats (SSRs), 18 tandem repeats, and 191 dispersed repeats distributed throughout the mitochondrial genome. RNA editing prediction revealed 394 putative editing sites, with notable enrichment in NADH dehydrogenase genes. Critical modifications included start codon conversion in atp6 (ACG → AUG) and stop codon alterations in ccmFc (CGA → UGA) and rpl16 (UAG → UAA). Comparative genomic analyses detected 50 chloroplast-derived DNA fragments, constituting 6.0% of the mitogenome, indicative of historical plastid-to-mitochondrion transfer events. Codon usage bias analysis demonstrated phenylalanine (Phe) as the most frequently encoded amino acid, with selection pressure identified as the predominant driver of codon usage patterns. Phylogenetic reconstruction employing 22 conserved PCGs resolved intra-ordinal relationships among eight Malpighiales families, revealing Phyllanthaceae sister to Salicaceae with robust nodal support. This study advances the utilization of mitochondrial genomes for elucidating phylogenetic relationships within Phyllanthus while providing essential genomic resources for future comparative mitogenomic investigations in Phyllanthaceae. The structural complexity revealed through repeat analyses and RNA editing patterns offers novel insights into plant mitochondrial genome evolution.
无根萍是大戟科的一员，是一种独特的漂浮水生植物，具有很高的观赏价值。在本研究中，我们组装了无根萍的线粒体基因组，这是大戟科首个线粒体基因组报告。该线粒体基因组由两条环状染色体组成，分别为230,785 bp（染色体1）和143,421 bp（染色体2），共包含32个蛋白质编码基因（PCG）、25个tRNA基因、4个rRNA基因和1个假基因。结构分析确定了118个简单序列重复（SSR）、18个串联重复和191个分散重复，分布于整个线粒体基因组中。RNA编辑预测显示有394个推定编辑位点，在NADH脱氢酶基因中显著富集。关键修饰包括atp6的起始密码子转换（ACG→AUG）以及ccmFc（CGA→UGA）和rpl16（UAG→UAA）的终止密码子改变。比较基因组分析检测到50个叶绿体衍生的DNA片段，占线粒体基因组的6.0%，表明存在历史上的质体到线粒体的转移事件。密码子使用偏好分析表明苯丙氨酸（Phe）是编码最频繁的氨基酸，选择压力被确定为密码子使用模式的主要驱动因素。利用22个保守PCG进行的系统发育重建解析了八个金虎尾目科之间的目内关系，揭示大戟科与杨柳科为姐妹关系，节点支持度很高。本研究推动了线粒体基因组在阐明叶下珠属系统发育关系方面的应用，同时为大戟科未来的比较线粒体基因组研究提供了重要的基因组资源。通过重复分析和RNA编辑模式揭示的结构复杂性为植物线粒体基因组进化提供了新的见解。
