Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, People's Republic of China.
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065 Chengdu, Sichuan, People's Republic of China.
Mol Phylogenet Evol. 2020 May;146:106737. doi: 10.1016/j.ympev.2020.106737. Epub 2020 Jan 23.
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
葱属（Allium L.）是单子叶植物中最大的属之一，广泛分布于北半球。已经使用许多形态和分子特征研究了葱属的基本系统发育。然而，在某些葱属组或节（如中国葱属的达吉斯坦组）中，形态特征可能与分子结果不一致，这可能导致物种关系不明确，并阻碍进一步的进化和适应性研究。在这里，收集了来自葱属达吉斯坦组的 6 种中国特有种的转录组序列，并提取了其单拷贝基因（SCGs）。使用串联和合并方法分析了种间关系。采用分支位点模型（BSM）检测了该组 5 个高地物种中的正选择基因（PSGs）。基于花、叶和花-叶组合中分别为 1644、1281 和 1580 个 SCGs，串联法生成了一个稳健一致且分辨率高的系统发育树。合并法中检测到个体基因树之间存在强烈冲突，形态特征与分子关系在某种程度上不一致。许多 PSGs 参与了各种应激和刺激（如缺氧、低温、干旱）、DNA 修复、代谢、营养或能量摄入、光合作用和信号转导的反应。我们的研究揭示了中国葱属达吉斯坦组特有种之间清晰的种间关系，并表明形态特征与分子关系的不匹配可能是由于前者比后者更容易趋同。我们的研究中检测到的 PSGs 可能为葱属物种的高原适应提供一些见解。
