背景:香附是沿海生态系统中的重要物种,具有经济和生态价值。为了阐明结构特征,变异,以及梭菌细胞器基因组的进化,我们测序了,组装,并比较了它的线粒体和叶绿体基因组。
结果:我们组装了梭菌的线粒体和叶绿体基因组。线粒体基因组(mtDNA)的总长度为927,413bp,GC含量为40.59%。它由两个圆形DNA组成,包括37个蛋白质编码基因(PCGs),22个tRNA,和五个rRNA。叶绿体基因组(cpDNA)的长度为186,204bp,包含93个PCG,40个tRNA,和8个rRNA。mtDNA和cpDNA包含81和129个串联重复,分别,和346和1,170个分散的重复,分别,两者都有270个简单的序列重复。细胞器基因组中第三个高频密码子(RSCU>1)倾向于A或U结束,而低频密码子(RSCU<1)倾向于在G或C结束。PCGs的RNA编辑位点相对较少,在mtDNA和cpDNA中只有9个和23个位点,分别。mtDNA中共有28个线粒体质体DNA(MTPT)来源于cpDNA,包括三个完整的trnT-GGU,trnH-GUG,和trnS-GCU.系统发育和共线性表明,蛇床子和圆周子之间的关系最密切。线粒体rns基因表现出最大的核苷酸变异性,而核苷酸变异性最大的叶绿体基因是infA。细胞器基因组中的大多数PCGs是负选择的,并且在进化上高度保守。只有6个线粒体基因和2个叶绿体基因显示Ka/Ks>1;atp9,atp6和rps7可能已经经历了潜在的正选择。
结论:我们组装并验证了C.stoloniferus的mtDNA,它包含一个15,034bp的反向互补序列。梭菌的细胞器基因组序列为物种鉴定提供了宝贵的基因组资源,进化,和莎草科的比较基因组研究。
BACKGROUND: Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.
RESULTS: We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.
CONCLUSIONS: We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.