Comparative analysis of complete chloroplast genome sequences of five endangered species and new insights into phylogenetic relationships of Paris
Comparative analysis of complete chloroplast genome sequences of five endangered species and new insights into phylogenetic relationships of Paris
复制标题
五种濒危物种叶绿体基因组全序列比较分析及巴黎系统发育关系新见解
DOI：
10.1016/j.gene.2022.146572
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发表时间：
2022-05-25
期刊：
影响因子：
3.5
通讯作者：
Duan, Baozhong
中科院分区：
文献类型：
--
作者：
Jiang, Yuan;Miao, Yujing;Duan, Baozhong
巴黎属植物是中国两千多年来珍贵的传统草本植物。然而，由于过度开发和栖息地破坏，巴黎正面临灭绝的威胁。相似的形态特征引起了巴黎种的分类争议。叶绿体（cp）基因组方法已被用于研究巴黎的进化。然而，一些研究证实，由于cp基因组的长度变化、缺口/索引缺失以及序列进化模型的不正确，可能会导致错误的关系。因此，迫切需要重建系统发育关系并开发遗传标记来保护这些物种。近年来的研究表明，蛋白质编码基因在系统发育研究中可以提供更好的系统发育关系。本研究鉴定了5个物种的cp全基因组，5个cp全基因组长度在162927 ~ 165267 bp之间，包含89个蛋白质编码基因、38个tRNA和8个rRNA。重复序列分析、密码子使用、rna编辑位点分析和cp基因组比较具有高度的保守性。基于蛋白质编码基因，系统发育树证实了Paris在Melanthiaceae目中的地位，为Paris sensu strict亚属（Paris s.s.）与Daiswa和Trillium的姐妹关系提供了最大的支持。此外，分子钟显示，Paris亚属起源于约52.81 Mya， Daiswa亚属起源于约24.56 Mya，这与系统发育调查结果一致。该研究为深入了解黑蜂科植物cp基因组结构的进化动态提供了有价值的依据，同时也为巴黎属植物的生物勘探和保护提供了依据。
Paris L. genus has been a precious traditional herb for more than 2000 years in China. However, due to overexploitation and habitat destruction, Paris is threatened by extinction. Similar morphological features cause the classification of Paris species in dispute. The chloroplast (cp) genome approach has been used to investigate the evolution of Paris. However, some studies confirm that the cp genome may result in misleading relationships because of the length variation, gaps/indels deletion, and incorrect models of sequence evolution in concatenated datasets. Therefore, there is a high demand for a reconstructed phylogenetic relationship and developed genetic markers to conserve these species. Recent studies have demonstrated that the protein-coding genes could provide a better phylogenetic relationship in the phylogenetic investigation. In this study, the complete cp genomes of five species were characterized, and the length of five cp genomes ranges from 162,927 bp to 165,267 bp, covering 89 protein-coding genes, 38 tRNA, and eight rRNA. The analysis of the repeat sequences, codon usage, RNA-editing sites, and comparison of cp genomes shared a high degree of conservation. Based on the protein-coding genes, the phylogenetic tree confirmed Paris's position in the order Melanthiaceae, providing maximum support for a sister relationship of the subgenera Paris sensu strict (Paris s.s.) with the Daiswa and Trillium. In addition, the molecular clock showed that subgenus Paris was inferred to have occurred at about 52.81 Mya, whereas subgenus Daiswa has originated at 24.56 Mya, which was consistent with the phylogenetic investigation. This study provided a valuable insight into the evolutionary dynamics of cp genome structure in the family Melanthiaceae, and it also contributes to the bioprospecting and conservation of Paris species.