Mushroom functional genomics springs up

Synthetic and Systems Biology Unit, Institute of Biochemistry Biological Research Center, Szeged, Hungary *Correspondence: lnagy@fungenomelab.com (L. N.) Received: March 1, 2023; Accepted: May 6, 2023; Published Online: June 5, 2023; https://doi.org/10.59717/j.xinn-life.2023.100005 © 2023 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Citation: Nagy LG. (2023). Mushroom functional genomics springs up. The Innovation Life 1(1), 100005. Mushroom science and its most broadly applied aspect, the production of edible and medicinal mushrooms, has traditionally synthesized knowledge from developmental biology, genetics, studies of fungal metabolism and a great deal of empirical knowledge accumulated over the centuries of practice in mushroom production. With the advent of high-throughput -omics, the field has quickly embraced new technologies, including genome and transcriptome sequencing or proteomics. However, important stepping stones both in terms of technology and knowledge for linking the genes and gene expression patterns to phenotypes, have been missing. A handful of studies, all published recently, forecast a change in this respect and portrays mushroom developmental biology coming of age. Genomic and transcriptomic resources have, as of today, been generated for many of the important mushroom-forming species in the Agaricomycetes, with a focus on fruiting body development and wood-decay, among others, and overall yielded information on the gene repertoires of most major species utilized by the mushroom industry, as well as related modeland non-model species (reviewed recently ). However, both approaches have their limitations in revealing precise gene function. Since a considerable portion of research on mushroom-forming fungi focuses on fruiting body development, which is a developmental process involving the temporal and spatial coordination of cellular events, understanding patterns of gene expression regulation and revealing the precise function of genes is key. This in turn requires forward/reverse genetics and functional genomics approaches (Figure 1), a field where a recent wave of papers have made significant progress. In a paper published recently in mBio, 2 identified the first cellulose-degradation related transcription factor in the Basidiomycota, Roc1 of Schizophyllum commune. They identified it by comparing RNA-Seq profiles of woodgrown and cellulose-grown cultures and found that the gene is conserved in the Agaricomycetes (although its possibly even more conserved and orthologous to ACE3 from Trichoderma reesei). Given the early emergence of Roc1, its origin may precede the emergence of efficient wood decay systems some ~300 million years ago. The roc1 knockout mutant showed highly reduced growth on cellulose (Avicel), cellobiose and xylan, but not on other carbon sources, suggesting that Roc1 is regulating genes involved in the utilization of these carbon sources. Indeed, several CAZyme genes were no longer upregulated when the mutant was grown on cellulose and ChIP-Seq analyses identified peaks associated with several CAZyme-encoding genes such as lytic polysaccharide monooxygenases, GH3 and GH5, which are typically associated with cellulose degradation.