Qi Jianzhao, Kang Shijie, Zhang Ming, Qi Shen, Li Yulai, Vadim Khassanov, Du Shuangtian, Li Minglei
Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China.
Center of Edible Fungi, Northwest A&F University, Yangling, Xianyang 712100, China.
J Fungi (Basel). 2025 May 20;11(5):395. doi: 10.3390/jof11050395.
mushrooms, common bulk edible fungi, have considerable culinary and medicinal value. The Qinling region, represented by Zhashui County, is the main production area of mushrooms in China. In this study, two wild strains, M12 and M13, selected from the Qinling region for their desirable horticultural traits after domestication, were sequenced and characterized. Sequencing assembly results based on Illumina NovaSeq and PacBio Sequel II HiFi showed that the M12 genome was 56.04 Mbp in size, with 2.58% heterozygosity and 14.13% repetitive sequences, and was anchored on 12 chromosomes using HI-C technology. In contrast, the M13 genome was 52.10 Mbp, showed 2.34% heterozygosity, 13.89% repetitive sequences, and was assembled into 12 scaffolds. Collinearity analysis revealed extensive homologous regions between the M12 and M13 genomes. Phylogenetic analysis suggested that the divergence between M12 and M13 occurred approximately 4.575 million years ago (MYAs), while their divergence from TFB-10046 SS5 occurred approximately 33.537 MYAs. Analyses of CYP450, carbohydrate-active enzymes (CAZymes), and gene family expansion/contraction revealed distinct genomic features between the two strains. SSR and LTR insertion time analyses revealed the genome dynamics of the two strains during their evolution. Analysis of secondary metabolite-associated biosynthetic gene clusters (BGCs) provides powerful clues to understand the origin of bioactive compounds in the mushroom. This work represents the first genome sequencing of the species derived from the Qinling region. These results not only enriched our understanding of the genome but also provided an important genomic resource and theoretical basis for the subsequent genetic breeding, functional gene mining, and development of medicinal components of species.
蘑菇作为常见的大宗可食用真菌，具有相当高的烹饪和药用价值。以柞水县为代表的秦岭地区是中国蘑菇的主要产区。在本研究中，从秦岭地区选取了两个野生菌株M12和M13，它们在驯化后具有优良的园艺性状，并对其进行了测序和特征分析。基于Illumina NovaSeq和PacBio Sequel II HiFi的测序组装结果表明，M12基因组大小为56.04 Mbp，杂合度为2.58%，重复序列为14.13%，并使用Hi-C技术将其锚定在12条染色体上。相比之下，M13基因组大小为52.10 Mbp，杂合度为2.34%，重复序列为13.89%，并组装成12个支架。共线性分析揭示了M12和M13基因组之间广泛的同源区域。系统发育分析表明，M12和M13之间的分化发生在大约457.5万年前（百万年前），而它们与TFB - 10046 SS5的分化发生在大约3353.7万年前。对细胞色素P450、碳水化合物活性酶（CAZymes）和基因家族扩增/收缩的分析揭示了这两个菌株之间不同的基因组特征。SSR和LTR插入时间分析揭示了这两个菌株在进化过程中的基因组动态。对次生代谢物相关生物合成基因簇（BGCs）的分析为理解蘑菇中生物活性化合物的起源提供了有力线索。这项工作代表了来自秦岭地区该物种的首次基因组测序。这些结果不仅丰富了我们对该基因组的认识，也为后续该物种的遗传育种、功能基因挖掘和药用成分开发提供了重要的基因组资源和理论基础。
