Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative genomics and pathway analyses of Agaricales species. The draft, generated from both next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing platforms to overcome high genetic heterozygosity, is composed of a 56.5 Mb sequence and 15,384 predicted genes. This mushroom possesses a complex reproductive system, including tetrapolar heterothallic and secondary homothallic mechanisms, and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources. Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances, including B vitamins, unsaturated fatty acids, and N-acetylglucosamine. RNA-seq data show that A. cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage, whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis. These results reflect diverse functions of the two anatomical structures of the fruiting body. Our comprehensive genomic and transcriptomic data, as well as preliminary comparative analyses, provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.

食用蘑菇Agrocybe cylindracea因其丰富的营养和风味而被广泛种植，据报道其许多代谢产物具有有益作用，例如对肿瘤和慢性疾病的药用作用。然而，缺乏基因组信息阻碍了对该真菌的进一步分子研究。在这里，我们提出了A. cylindracea的基因组装配以及比较菌种的基因组学和通路分析。该草案由下一代测序（NGS）和单分子实时（SMRT）测序平台生成，可克服高遗传杂合性，由56.5 Mb序列和15,384个预测基因组成。该蘑菇拥有复杂的生殖系统，包括四极异硫杂和二级同硫杂化机制，并具有多个水解酶和肽酶，可逐步有效地降解各种碳源。我们的途径分析揭示了多糖和其他活性物质（包括B维生素，不饱和脂肪酸和N-乙酰氨基葡萄糖）的生物合成中涉及的复杂过程。RNA-seq数据显示圆环曲霉梭菌倾向于合成用于碳封存和能量存储的碳水化合物，而pilei在碳利用和不饱和脂肪酸的生物合成中更活跃。这些结果反映了子实体的两个解剖结构的不同功能。我们全面的基因组和转录组数据，以及初步的比较分析，可就活性化合物和营养成分方面的药物作用分子细节提供深刻见解。