Melilotus species are used as green manure and rotation crops worldwide and contain abundant pharmacologically active coumarins. However, there is a paucity of information on its genome and coumarin production and function. Here, we reported a chromosome-scale assembly of Melilotus albus genome with 1.04 Gb in eight chromosomes, containing 71.42% repetitive elements. Long terminal repeat retrotransposon bursts coincided with declining of population sizes during the Quaternary glaciation. Resequencing of 94 accessions enabled insights into genetic diversity, population structure, and introgression. Melilotus officinalis had relatively larger genetic diversity than that of M. albus. The introgression existed between M. officinalis group and M. albus group, and gene flows was from M. albus to M. officinalis. Selection sweep analysis identified candidate genes associated with flower colour and coumarin biosynthesis. Combining genomics, BSA, transcriptomics, metabolomics, and biochemistry, we identified a β-glucosidase (BGLU) gene cluster contributing to coumarin biosynthesis. MaBGLU1 function was verified by overexpression in M. albus, heterologous expression in Escherichia coli, and substrate feeding, revealing its role in scopoletin (coumarin derivative) production and showing that nonsynonymous variation drives BGLU enzyme activity divergence in Melilotus. Our work will accelerate the understanding of biologically active coumarins and their biosynthetic pathways, and contribute to genomics-enabled Melilotus breeding.

中文翻译：

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Melilotus albus 的基因组和系统生物学提供了对香豆素生物合成的见解

椴树种在世界范围内被用作绿肥和轮作作物，含有丰富的药理活性香豆素。然而，关于其基因组和香豆素生产和功能的信息很少。在这里，我们报告了在 8 条染色体中具有 1.04 Gb 的Melilotus albus基因组的染色体规模组装，其中包含 71.42% 的重复元素。长末端重复逆转录转座子爆发与第四纪冰期人口规模的下降相吻合。对 94 份材料的重新测序使我们能够深入了解遗传多样性、种群结构和基因渗入。厚朴的遗传多样性比M. albus大。M. officinalis之间存在基因渗入M. albus 组和M. albus组，基因流从M. albus到M. officinalis。选择扫描分析确定了与花色和香豆素生物合成相关的候选基因。结合基因组学、BSA、转录组学、代谢组学和生物化学，我们确定了一个有助于香豆素生物合成的 β-葡萄糖苷酶 (BGLU) 基因簇。MaBGLU1功能通过在M. albus中的过表达、在大肠杆菌中的异源表达和底物喂养得到验证，揭示了它在东莨菪碱（香豆素衍生物）生产中的作用，并表明非同义变异驱动了苜蓿中 BGLU 酶活性的差异. 我们的工作将加速对具有生物活性的香豆素及其生物合成途径的理解，并为基因组学支持的Melilotus育种做出贡献。