Table 4 Summary of transcriptomics studies/transcriptomics combined with proteomics studies on medicinal mushrooms

C. militaris

Genome-wide transcriptome and proteome investigation

Variations in gene expression between the mycelia and fruiting bodies

Gene expression comparison in different developmental stages

[181]

C. militaris

Transcriptomics

•L-alanine’s effect on cordycepin biosynthesis at a molecular level

•Genes of rate-limiting enzymes in energy production pathways and amino acid conversion

•Cordycepin network

Uncovering mechanisms, their associated genes, and transcription factors

Achieving metabolic network maps from the substrate to the desired product

Increasing the yields of bioactive metabolites and improving strain breeding

[198]

C. militaris

Transcriptomics

•Carotenoids production

•Biosynthetic pathway of carotenoids and its related genes

Improving the production of bioactive metabolites

Elucidating biosynthetic pathways of bioactive metabolites and their associated genes

[199]

Cordyceps kyushuensis

Transcriptomics and proteomics

Gene clusters associated with the production of cordycepin and pentostatin

Identification of gene clusters and functional proteins associated with the production of bioactive metabolites

Improving the yield of bioactive metabolites

[225]

G. lucidum

Comparative transcriptome analysis

•Comparing DEGs in liquid static culture and shaking culture

•Synthesis of ganoderic acids and asexual spores

Providing beneficial data for large-scale synthesis of bioactive compounds

[200]

G. lucidum

Transcriptomics

•Mushroom development and growth

•Adjustment of secondary metabolic biosynthetic pathways

Elucidating the effect of transcriptional plasticity

[190]

G. lucidum

Transcriptomics

Functional genes of the wood degradation and terpenoid pathway

Providing a basis for conducting functional genomics research

[180]

G. lucidum

Transcriptomics

Mitochondrial DNA

Offering more information about the functions and evolution of fungal mitochondrial DNA

[182]

Copper-induced lignocellulolytic G.lucidum MDU-7

Transcriptomics and proteomics

Lignocellulose breakdown and terpenoid biosynthetic routes

Uncovering genes related to different pathways

[226]

V. volvacea

Transcriptomics

Stipe development and switching from egg to elongation stage

Providing a better understanding of the changes during different developmental stages

[183]

P. eryngii

Transcriptomics

•Transcriptional response to considerable levels of heavy metals

•Mechanism of NO in increasing heavy metal tolerance

•Coincidence of secondary metabolite production inhibition with the increase in carbohydrate metabolism and the rate of energy

Offering data regarding transcriptional responses to different environmental conditions

Uncovering mechanisms

[186]

P. eryngii

Transcriptomics and proteomics

Cd²⁺ stress

Providing insights into the genes and proteins related to different stressful conditions

[186]

O.sinensis

Developmental transcriptomics

Hub genes and main routes in the development process

Providing insights into the gene profiles related to sexual development

[189]

O.sinensis

Transcriptomics

Modulating signal transduction and the level of transcription in fruiting body development

Cordycepin biosynthetic pathway

Providing models for the synthesis of bioactive metabolites

Uncovering genes and investigating important biosynthetic and developmental pathways

[185]

H. erinaceus

Transcriptomics

Terpenoid biosynthesis in mycelia

Polyketides biosynthesis in the fruiting body

Providing insights into the expression and regulation of biosynthetic genes in different developmental phases

[10]

H. erinaceus

Transcriptomics and proteomics

Regulation of bioactive metabolites

Offering information about the genes and proteins involved in the regulation of bioactive metabolites

[220]

A. cinnamomea

Transcriptomics

Production of secondary metabolites with medicinal properties

Identification of DEGs between fruiting bodies and mycelia

Providing beneficial data for enhancing the production of valuable metabolites

[97]

T. albuminosus

Transcriptomics

Saponin biosynthesis

Identification of enzymes related to the biosynthesis of bioactive compounds

[187]

L. edodes

Transcriptomics

•Light-induced formation of Brown film (BF)

•Secondary metabolite biosynthesis

•Gene expression and gene regulation mechanisms

Uncovering molecular mechanisms

Helping further functional and pathway analysis

[188]

L. edodes

Transcriptomics and proteomics

Temperature stress

Offering information about the genes and proteins associated with different stresses

[219]

M. importuna

Transcriptomics and proteomics

Decomposition of exogenous nutrient bag

Providing information about the genes and proteins

[218]

S. commune

Transcriptomics and proteomics

Special odor formation

Providing data regarding the genes and proteins

[221]

F. velutipes

Transcriptomics and proteomics

Development of the fruiting body

Providing information about the genes and proteins

[222]

D. indusiata

Transcriptomics and proteomics

Development of the fruiting body

Providing information about the genes and proteins

[223]

T. guangdongense

Transcriptomics and proteomics

•Development and growth

•Regulation of terpenoid, polysaccharide, ergosterol, and adenosine production-related proteins during the development

Indicating the significance of post-transcriptional procedures

Investigating mechanisms of development in fungi at the molecular level

Improving cultivation techniques

[104]

L. rhinocerotis

Transcriptomics

Secondary metabolite routes and little cysteine-rich proteins in the sclerotium

Discovering genes with considerable expression

[169]

Agrocybe aegerita

Transcriptomics and proteomics

Production and synthetic pathways of polysaccharides and sterol

Elucidating biosynthetic pathways

Providing beneficial data for constructing mushroom cell factories in the future

[129]