PDF(Pubmed)
Abstract：
Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.
摘要：
Meliaazedarach是制药行业中具有巨大价值的物种。尽管已经探索了M.azedarach的叶绿体基因组，线粒体基因组（Mt基因组）的信息仍然令人惊讶地有限。在这项研究中,我们使用BGI短读段和Nanopore长读段的混合组装策略来组装M.azedarach的Mt基因组。M.azedarach的Mt基因组的特征是两个圆形染色体，长度为350,142bp和290,387bp，分别,编码35个蛋白质编码基因（PCGs），23个tRNA基因，和3个rRNA基因。一对直接重复序列（R1和R2）与基因组重组相关，基于Sanger测序和Oxford纳米孔测序产生两种构象。比较分析确定了Mt和叶绿体基因组之间的19个同源片段，最长的片段为12,142bp。基于PCGs的系统发育分析与被子植物系统发育组的最新分类组成。值得注意的是,基于35个PCGs，总共预测了356个潜在的RNA编辑位点，编辑事件导致rps10基因中的终止密码子和nad4L和atp9基因中的起始密码子的形成，经PCR扩增和Sanger测序验证。一起来看,对M.azedarach无间隙Mt基因组的探索为进化研究和复杂的有丝分裂基因组结构提供了新的见解。
