Dissecting Metabolic Regulation in Mycelial Growth and Fruiting Body Developmental Stages of Cordyceps militaris through Integrative Transcriptome Analysis

Kim

et al. 2023

Front. Fungal Biol.

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

Section: The Need For the Evolutionary Integration Of Multiple Modelsmentioning

confidence: 99%

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics

Kim

et al. 2023

Front. Fungal Biol.

“…The transcriptome profiles of C. militaris at specific developmental stages are distinct (Table 3) [48]. Differentially expressed gene (DEG) analysis was performed, and a transcription-level comparison between mycelia and fruiting bodies showed significant differences: C. militaris TBRC6039 had 1877 DEGs, among which 935 and 942 genes were up-regulated in the mycelia and fruiting bodies, respectively [49]. In addition, genes involved in lipid metabolism were up-regulated in fruiting bodies compared to mycelia.…”

Section: Militaris Transcriptome Analysismentioning

confidence: 99%

Research Progress in Understanding the Molecular Biology of Cordyceps militaris

Wang,

Li,

Tian

et al. 2024

Fermentation

Cordyceps militaris (C. militaris) is a valued medicinal fungus that can be traced back thousands of years in traditional Chinese medicine (TCM). Both TCM and modern scientific research have confirmed the positive effects of C. militaris on human health. In recent years, C. militaris has gained wide popularity; unfortunately, strains often degrade during cultivation, resulting in a decline in fruiting bodies and active components that negatively impacts the development of C. militaris in the health food and medicine industries. This review summarizes the current progresses in research on the genomic, transcriptomic, proteomic, and genetic manipulation of C. militaris and discusses its primary metabolites and strain degradation mechanisms. The current challenges and future prospects of C. militaris research are also discussed.

“…Due to the discrimination in phenotypic characteristics between the wild-type and disruptant strains in the active growth phase, which is the stage when metabolism is active [50], we collected the cells after 11 h of cultivation time under dark conditions, which had the maximum specific growth rates (Table 1), to investigate their global transcriptional responses. The transcriptome analysis of WJ11 and ∆carRP WJ11 strains showed that raw reads were obtained at an average sequencing depth of 43.82 million reads.…”

Section: Transcriptome Data and Degs Across Pairwise Comparisons Of W...mentioning

confidence: 99%

Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis

Li,

Thananusak,

Raethong

et al. 2024

Biology

Self Cite

Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain’s economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology.