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.
柱状田头菇（A. cylindrace），隶属于真菌界，担子菌门，伞菌目，是常见的可食用真菌，在亚洲地区被广泛种植。本项研究利用全基因组测序数据，获得了约56.5Mb较高质量的基因组草图，预测了15,384个蛋白编码基因，阐述了A. cylindracea基因组序列的基本特征、潜在的生殖方式、伞菌目真菌中的进化地位以及营养物质合成的组学基础并构建了A. cylindrace活性物质的代谢通路图。研究发现A. cylindrace基因组中包含丰富的碳水化合物水解酶、蛋白酶以及有效降解植物细胞壁所需多种酶用于降解和利用外源物质提供能量。转录组分析发现A. cylindrace伞柄部分糖类物质合成相关基因及碳水化合物代谢通路上表达更为活跃，而在其伞盖部分则表现出利用碳源合成不饱和脂肪酸等物质的能力。同时基因表达谱反映了代谢途径中一些关键基因的表达特征。





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