College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China.
BMC Genomics. 2024 Sep 12;25(1):853. doi: 10.1186/s12864-024-10765-6.
Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported.
In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes.
This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.
永泰水韭是水韭科的一种水生开花植物，具有显著的适应特性，使其能够在淹没、动荡的栖息地中生存。尽管该科的叶绿体基因组信息不断扩展，但线粒体基因组序列尚未报道。
在本研究中，我们对永泰水韭的线粒体基因组进行了特征描述，其基因组为圆形，大小为 426928bp，编码 31 个蛋白质编码基因（PCGs）、18 个 tRNA 和 3 个 rRNA 基因。我们的综合分析集中在基因内容、重复序列、RNA 编辑过程、细胞内基因转移、系统发育和密码子使用偏好上。鉴定出许多重复序列，包括 130 个简单序列重复、22 个串联重复和 220 个分散重复。系统发育分析将永泰水韭（水韭科）置于 Malpighiales 目中，与 Calophyllaceae 科关系密切，这与 APG IV 分类一致。与其他 9 种 Malpighiales 物种的比较分析显示了可变和保守区域，为该目中的基因组进化提供了深入了解。值得注意的是，永泰水韭的 GC 含量明显低于其他 Malpighilales，主要是由于非编码区域和特定蛋白质编码基因（特别是 nad 基因）的变化。值得注意的是，RNA 编辑位点数量较少（276 个），分布在 27 个 PCGs 上不均匀。dN/dS 分析表明，只有永泰水韭的 ccmB 基因受到正选择，该基因在细胞色素 c 生物合成中起着关键作用。此外，永泰水韭的线粒体和叶绿体基因组之间存在 13 个含有基因的同源区域，表明这两个细胞器基因组之间存在基因转移事件。
本研究组装并注释了 Podostemaceae 科的第一个线粒体基因组。线粒体基因组成、GC 含量和 RNA 编辑位点的比较结果为这一水生真双子叶植物群的适应特征和遗传重编程提供了新的见解，并为未来研究 Podostemaceae 科和 Malpighiales 目中相关植物科的基因组进化和适应机制提供了基础。
