Zhang Shuo, Chang Shengxin, Lin Xinge, Xu Shisong, Leng Qingyun, Li Haiyan, López Hernán Ariel, Yin Junmei, Wu Zhiqiang, Niu Junhai
National Key Laboratory for Tropical Crop Breeding/Key Laboratory of Gene Resources and Germplasm Enhancement in Southern China, MARA/Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan Province, 571101, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
BMC Genomics. 2025 Aug 4;26(1):722. doi: 10.1186/s12864-025-11891-5.
Plant organellar genomes play a crucial role in metabolism and adaptation. In this study, the organellar genomes and transcriptome of (Nyctaginaceae) were sequenced and assembled using PacBio sequencing and strand-specific RNA sequencing, respectively. Structural and evolutionary comparisons of the plastidial and mitochondrial genomes (plastome and mitogenome) were conducted among and five other taxa within Caryophyllales to elucidate the similarities and divergences between these two organellar genomes at a detailed level. The plastome of was assembled into a 154.7 kb circular molecule with a typical quadripartite structure, while the mitogenome was assembled into three stable circular molecules measuring 160.7 kb, 97.6 kb, and 64.3 kb, respectively. Reconstruction of the organellar transcripts revealed extensive transcriptional activity in the non-coding regions of the organellar genomes. However, the transcriptional activity and editing proportions of novel transcripts identified in these regions were significantly lower compared to those of conserved organellar transcripts. A tenfold difference in the number of RNA editing sites was observed between plastidial and mitochondrial transcripts (43 vs. 453), with the majority (70%) of these sites located at nonsilent sites within coding regions, exhibiting high editing efficiency (> 70%). The turnover rate of Caryophyllales mitogenomes was found to be, on average, 6.1 times faster than that of plastomes. In contrast, the nucleotide substitution rate in protein-coding genes was significantly higher in plastomes than in mitogenomes. Moreover, nonsilent nucleotide substitutions in genes encoding components of the electron transfer chain were more constrained compared to those in ribosomal protein-coding genes in both plastidial and mitochondrial genomes of Caryophyllales. Together, these findings provide vital genetic resources that enhance our understanding of the dynamic evolution and phylogenetic relationships within and the broader Caryophyllales order.
The online version contains supplementary material available at 10.1186/s12864-025-11891-5.
植物细胞器基因组在代谢和适应性方面发挥着关键作用。在本研究中，分别使用PacBio测序和链特异性RNA测序对紫茉莉科（Nyctaginaceae）的细胞器基因组和转录组进行了测序和组装。在紫茉莉科与石竹目其他五个分类群之间对质体基因组和线粒体基因组（质体基因组和线粒体基因组）进行了结构和进化比较，以详细阐明这两个细胞器基因组之间的异同。紫茉莉科的质体基因组被组装成一个154.7 kb的环状分子，具有典型的四分体结构，而线粒体基因组被组装成三个稳定的环状分子，分别为160.7 kb、97.6 kb和64.3 kb。细胞器转录本的重建揭示了细胞器基因组非编码区广泛的转录活性。然而，与保守的细胞器转录本相比，在这些区域鉴定出的新转录本的转录活性和编辑比例显著较低。在质体和线粒体转录本之间观察到RNA编辑位点数量相差十倍（43个与453个），其中大多数（70%）位点位于编码区内的非沉默位点，表现出高编辑效率（>70%）。发现石竹目线粒体基因组的周转速率平均比质体基因组快6.1倍。相比之下，质体基因组中蛋白质编码基因的核苷酸替换率显著高于线粒体基因组。此外，在石竹目质体和线粒体基因组中，编码电子传递链成分的基因中的非沉默核苷酸替换比核糖体蛋白编码基因中的更受限制。总之，这些发现提供了重要的遗传资源，增强了我们对紫茉莉科及更广泛的石竹目内动态进化和系统发育关系的理解。
在线版本包含可在10.1186/s12864-025-11891-5获取的补充材料。
