{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T05:01:19Z","timestamp":1791608479239,"version":"4.3.4"},"reference-count":75,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,20]],"date-time":"2025-12-20T00:00:00Z","timestamp":1766188800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Innovation Project of the Chinese Academy of Medical Sciences","award":["2021-I2M-1-031"],"award-info":[{"award-number":["2021-I2M-1-031"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Carbon dioxide (CO2) is a key environmental factor that regulates the morphology of fruiting bodies in edible fungi. High CO2 concentrations often lead to the formation of antler-shaped abnormal fruiting bodies in Ganoderma lucidum. Yet, the molecular response mechanisms underlying this process remain unclear. To address this gap, this study integrated transcriptomics and untargeted metabolomics to compare the transcriptional and metabolic profiles of G. lucidum fruiting bodies at three growth stages, cultivated under both normal (0.04%) and high CO2 concentrations (0.3%). Metabolomic analysis revealed that, compared to the control groups, 387, 337, and 445 differentially accumulated metabolites were identified in the elevated-CO2 groups, respectively. Moreover, high CO2 concentrations led to a widespread down-regulation of various amino acids biosynthesis, accompanied by a marked accumulation of specific triterpenoids and steroids. This indicates distinct metabolite accumulation patterns in the fruiting bodies of G. lucidum cultivated under elevated CO2. Furthermore, transcriptomic analysis showed that, at a key stage of fruiting body development, high CO2 concentrations adversely affected gene expression of cell cycle-yeast, proteasome, DNA replication, mismatch repair, and meiosis-yeast pathways, which may decrease the cell division ability and prevent normal pileus development. Meanwhile, the differential expression of genes related to CO2 signal perception and transduction and cell wall remodeling provided a molecular basis for the morphogenesis of the antler-type fruiting bodies. Overall, this study delineates a multi-layered, multi-pathway regulatory network through which high CO2 concentrations affect the development and metabolism of G. lucidum, encompassing energy metabolism reprogramming, inhibition of cell division, and cell wall remodeling. This provides new insights into CO2 as an environmental signal in fungal development and a theoretical basis for optimizing G. lucidum cultivation practices.<\/jats:p>","DOI":"10.3390\/jof12010005","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T14:27:47Z","timestamp":1766500067000},"page":"5","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Combined Transcriptomic and Metabolomic Analyses of the Response of Ganoderma lucidum to Elevated CO2"],"prefix":"10.3390","volume":"12","author":[{"given":"Tingting","family":"Fang","sequence":"first","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Yao","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Li","sequence":"additional","affiliation":[{"name":"Fujian Xianzhilou Biological Science and Technology Co., Ltd., Fuzhou 300057, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guohui","family":"Liu","sequence":"additional","affiliation":[{"name":"Fujian Xianzhilou Biological Science and Technology Co., Ltd., Fuzhou 300057, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaofeng","family":"Wu","sequence":"additional","affiliation":[{"name":"Fujian Xianzhilou Biological Science and Technology Co., Ltd., Fuzhou 300057, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Lan","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangdong","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6030","DOI":"10.1002\/ptr.7215","article-title":"Ganoderma lucidum (Reishi) an edible mushroom; a comprehensive and critical review of its nutritional, cosmeceutical, mycochemical, pharmacological, clinical, and toxicological properties","volume":"35","author":"Ahmad","year":"2021","journal-title":"Phytother. 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