School of Biological Science, Guizhou Education University, Guiyang, 550018, China.
Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, 550018, China.
BMC Genomics. 2024 Mar 8;25(1):260. doi: 10.1186/s12864-024-10136-1.
In this study, we conducted an assembly and analysis of the organelle genomes of Aconitum carmichaelii. Our investigation encompassed the examination of organelle genome structures, gene transfer events, and the environmental selection pressures affecting A. carmichaelii. The results revealed distinct evolutionary patterns in the organelle genomes of A. carmichaelii. Especially, the plastome exhibited a more conserved structure but a higher nucleotide substitution rate (NSR), while the mitogenome displayed a more complex structure with a slower NSR. Through homology analysis, we identified several instances of unidirectional protein-coding genes (PCGs) transferring from the plastome to the mitogenome. However, we did not observe any events which genes moved from the mitogenome to the plastome. Additionally, we observed multiple transposable element (TE) fragments in the organelle genomes, with both organelles showing different preferences for the type of nuclear TE insertion. Divergence time estimation suggested that rapid differentiation occurred in Aconitum species approximately 7.96 million years ago (Mya). This divergence might be associated with the reduction in CO levels and the significant uplift of the Qinghai-Tibet Plateau (QTP) during the late Miocene. Selection pressure analysis indicated that the dN/dS values of both organelles were less than 1, suggested that organelle PCGs were subject to purification selection. However, we did not detect any positively selected genes (PSGs) in Subg. Aconitum and Subg. Lycoctonum. This observation further supports the idea that stronger negative selection pressure on organelle genes in Aconitum results in a more conserved amino acid sequence. In conclusion, this study contributes to a deeper understanding of organelle evolution in Aconitum species and provides a foundation for future research on the genetic mechanisms underlying the structure and function of the Aconitum plastome and mitogenome.
在这项研究中，我们对乌头属植物的细胞器基因组进行了组装和分析。我们的研究包括对细胞器基因组结构、基因转移事件以及影响乌头属植物的环境选择压力的研究。研究结果揭示了乌头属植物细胞器基因组的独特进化模式。特别是，质体基因组表现出更保守的结构，但核苷酸替代率（NSR）更高，而线粒体基因组则表现出更复杂的结构，NSR 更慢。通过同源分析，我们鉴定了几个从质体基因组单向转移到线粒体基因组的蛋白编码基因（PCG）。然而，我们没有观察到任何基因从线粒体基因组转移到质体基因组的事件。此外，我们在细胞器基因组中观察到多个转座元件（TE）片段，两个细胞器对核 TE 插入的类型表现出不同的偏好。分化时间估计表明，大约在 796 万年前，乌头属植物发生了快速分化。这种分化可能与中新世晚期 CO 水平降低和青藏高原（QTP）显著抬升有关。选择压力分析表明，两个细胞器的 dN/dS 值均小于 1，表明细胞器 PCG 受到纯化选择。然而，我们在 Subg. Aconitum 和 Subg. Lycoctonum 中没有检测到任何正选择基因（PSG）。这一观察结果进一步支持了这样的观点，即乌头属植物细胞器基因受到更强的负选择压力，导致更保守的氨基酸序列。总之，本研究有助于深入了解乌头属植物细胞器的进化，并为未来研究乌头属植物质体和线粒体基因组的结构和功能的遗传机制提供了基础。
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