Braseniaschreberi,传统上用于中药和烹饪的植物物种,代表开花植物(被子植物)的早期进化阶段。虽然该物种的质体基因组已经发表,它的线粒体基因组(有丝分裂基因组)尚未被广泛探索,明显缺乏对其细胞器基因组的全面比较分析。在我们的研究中,我们利用来自Illumina平台和OxfordNanopore的测序数据组装了B.schreberi的整个有丝分裂基因组。Schreberi有丝分裂基因组主要以六个环状DNA分子存在,最大的是628,257个碱基对(bp),最小的是110,220bp,总计1.49兆字节(Mb)。然后我们注释了B.schreberi的有丝分裂基因组。有丝分裂基因组包含总共71个基因:其中40个是编码蛋白质基因(PCGs),28个是用于转移RNA(tRNA)的基因,其余3个是核糖体RNA(rRNA)的基因。在密码子使用分析中,我们注意到每个氨基酸特有的独特密码子偏好。最常用的密码子表现出1.36的平均RSCU,表明密码子选择存在明显的偏倚。在重复序列分析中,共鉴定出553个简单序列重复序列(SSR),1,822个分散重复(包括1,015个正向重复和807个回文重复),和608个长末端重复(LTR)。此外,在分析细胞器基因组之间的同源序列时,我们检测到38个来自质体基因组的同源序列,每个超过500bp,在B.schreberi线粒体基因组中。值得注意的是,十个tRNA基因(trnC-GCA,trnM-CAU,trnI-CAU,trnQ-UUG,trnN-GUU,trnT-GGU,trnW-CCA,trnA-UGC,trnI-GAU,和trnV-GAC)似乎已从叶绿体完全转移到有丝分裂基因组。利用Deepred-mt预测有丝分裂基因组中的RNA编辑位点,我们在40个线粒体PCGs中鉴定出675个高质量RNA编辑位点.在我们研究的最后阶段,我们进行了共线性分析,并推断了Schreberi与其他被子植物的系统发育关系,利用线粒体PCGs作为基础。结果表明,蛇形芽孢杆菌有丝分裂基因组的非编码区具有丰富的重复序列和外源序列,施雷柏氏芽孢杆菌与Euryaleferox的关系更密切。
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.