Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
Sci Rep. 2024 Apr 29;14(1):9783. doi: 10.1038/s41598-024-58934-7.
The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.
多穗蓼亚科包含了大量具有重要经济价值的药用和园艺植物。然而，由于缺乏基于系统发育关系的强大分类学，这个科内的分类令人困惑，而且对于许多属于这个分类的植物的叶绿体基因组也缺乏报道。在这项研究中，我们通过测序和表征六种多穗蓼亚科植物（包括头状蓼、耳叶蓼、细梗蓼、何首乌、虎杖和五叶地锦）的完整叶绿体基因组进行了全面分析。我们的研究结果表明，这六种植物的叶绿体基因组具有典型的四分体结构，平均长度为 162931bp。比较叶绿体分析、密码子使用分析和重复序列分析表明，这些植物的叶绿体基因组具有高度的保守性。此外，系统发育分析揭示了头状蓼占据一个独特的分支，而细梗蓼与属于虎杖属的三种植物关系更为密切。基于最大似然树的选择压力分析表明，共有 14 个蛋白编码基因表现出正选择，其中 psbB 和 ycf1 具有最多的正氨基酸位点。此外，我们还鉴定了四个分子标记，即 petN-psbM、psal-ycf4、ycf3-trnS-GGA 和 trnL-UAG-ccsA，它们具有高度的变异性，可用于鉴定这六种植物。
