Xie Muyun, Wang Jing, Wang Feixiang, Wang Jinfeng, Yan Yunjin, Feng Kun, Chen Baixiong
School of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, China.
J Fungi (Basel). 2025 May 30;11(6):422. doi: 10.3390/jof11060422.
Edible fungi, a group of globally significant macrofungi, are highly valued for their unique flavors and substantial nutritional and medicinal properties. Understanding the molecular mechanisms governing their growth, development, gene function, biosynthesis of valuable compounds, and environmental adaptation is crucial for enhancing yield and quality, providing essential scientific support for industrial progress. Genomics, transcriptomics, and proteomics, as cornerstone life science technologies, offer powerful, integrated approaches to decipher genetic codes, reveal gene expression patterns, and elucidate complex metabolic networks in edible fungi. These advancements are transitioning research from traditional cultivation methods towards deeper molecular biology exploration. This review synthesizes key progress in applying genomics, transcriptomics, and proteomics to edible fungi, with a particular focus on metabolism-related research and the fundamentals of metabolic network construction. It discusses how these technologies, independently and in preliminary integration, uncover critical steps and regulatory mechanisms within endogenous metabolic pathways. While acknowledging the importance of metabolomics and epigenomics as cutting-edge areas, this review focuses on the "classical triad" of genomics, transcriptomics, and proteomics due to their technological maturity, data accessibility, and established application base in elucidating core metabolic mechanisms in edible fungi. The goal is to deepen the understanding of edible fungi metabolic mechanisms, providing a vital theoretical basis and practical insights for optimizing cultivation, enabling genetic improvement, harnessing bioactive substances, and promoting industrial upgrading, thereby boosting the overall efficiency and competitiveness of the edible fungi industry.
食用菌是一类在全球具有重要意义的大型真菌，因其独特的风味以及丰富的营养和药用价值而备受重视。了解其生长、发育、基因功能、有价值化合物的生物合成以及环境适应性的分子机制，对于提高产量和品质至关重要，可为产业发展提供重要的科学支撑。基因组学、转录组学和蛋白质组学作为生命科学的基础技术，为解读食用菌的遗传密码、揭示基因表达模式以及阐明复杂的代谢网络提供了强大的综合方法。这些进展正推动着食用菌研究从传统栽培方法向更深入的分子生物学探索转变。本文综述了基因组学、转录组学和蛋白质组学在食用菌研究中的关键进展，特别关注与代谢相关的研究以及代谢网络构建的基础。探讨了这些技术如何独立以及初步整合，揭示内源代谢途径中的关键步骤和调控机制。尽管认识到代谢组学和表观基因组学作为前沿领域的重要性，但由于基因组学、转录组学和蛋白质组学技术成熟、数据可及且在阐明食用菌核心代谢机制方面有既定的应用基础，本文重点关注这“经典三联体”。目的是加深对食用菌代谢机制的理解，为优化栽培、实现遗传改良、利用生物活性物质以及促进产业升级提供重要的理论基础和实践见解，从而提高食用菌产业的整体效率和竞争力。
