A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions
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...
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| Language: | English |
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MDPI AG
2025-05-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/11/6/422 |
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| author | Muyun Xie Jing Wang Feixiang Wang Jinfeng Wang Yunjin Yan Kun Feng Baixiong Chen |
| author_facet | Muyun Xie Jing Wang Feixiang Wang Jinfeng Wang Yunjin Yan Kun Feng Baixiong Chen |
| author_sort | Muyun Xie |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-714f26f4574b43d9adb89bf4ff731bb8 |
| institution | Matheson Library |
| issn | 2309-608X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj-art-714f26f4574b43d9adb89bf4ff731bb82025-06-25T14:02:04ZengMDPI AGJournal of Fungi2309-608X2025-05-0111642210.3390/jof11060422A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future DirectionsMuyun Xie0Jing Wang1Feixiang Wang2Jinfeng Wang3Yunjin Yan4Kun Feng5Baixiong Chen6School of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaSchool of Bioengineering, Zunyi Medical University, Jinwan Road No. 368, Zhuhai 519090, ChinaEdible 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.https://www.mdpi.com/2309-608X/11/6/422genomicstranscriptomicsproteomicsedible fungimetabolic networksbiosynthesis |
| spellingShingle | Muyun Xie Jing Wang Feixiang Wang Jinfeng Wang Yunjin Yan Kun Feng Baixiong Chen A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions Journal of Fungi genomics transcriptomics proteomics edible fungi metabolic networks biosynthesis |
| title | A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions |
| title_full | A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions |
| title_fullStr | A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions |
| title_full_unstemmed | A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions |
| title_short | A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions |
| title_sort | review of genomic transcriptomic and proteomic applications in edible fungi biology current status and future directions |
| topic | genomics transcriptomics proteomics edible fungi metabolic networks biosynthesis |
| url | https://www.mdpi.com/2309-608X/11/6/422 |
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