Table 2 Summary of the genomics studies on edible/medicinal mushrooms

Uncovering mechanisms and pathways

A. bisporus

Acclimatization to a humic-rich ecological niche in the process of plant degradation

Genetic and enzymatic procedures which control the acclimatization were elucidated

[130]

V. volvacea

•Degradation of the cultivating compost containing agricultural waste

•Sexual reproduction

•Susceptibility to low temperatures at the level of molecules

Many genes encoding enzymes associated with the degradation of cellulose, hemicellulose, and pectin were identified

[23]

S. commune

•Mushroom formation

•Wood-degrading machinery and its capability for breaking down lignocellulose

–

[131]

C. militaris

Medicinal compounds synthesis

–

[138]

G.sinense

•Secondary metabolism

•Different defense systems

More than thirty gene clusters associated with the biosynthetic pathways of secondary metabolites, as well as numerous genes contributing to their transport and regulation were identified

[139]

S. sanghuang

Secondary metabolites and their synthesis

334 carbohydrate-active enzymes coding, 343 transporters, and 4 velvet family proteins were identified

[140]

Tuber melanosporum

Evolutionary origins and symbiosis

–

[141]

L. edodes

Lignocellulose degradation

101 lignocellulolytic enzymes were determined and gave insights into the mechanism of lignocellulose degradation

[143]

P. eryngii

Lignin and cellulose degradation

The carbohydrate-active enzymes and oxidoreductases in its genome uncovered the mechanisms of cellulose and lignin bioconversion

[144]

A. cinnamomea

•Sexual development

•The production of sesquiterpenoids, antrocamphin, ergostanes, antroquinonol, and triterpenoids

DEGs between mycelia and fruiting bodies as well as 242 proteins in different bioactive metabolite pathways were determined

[97]

Identification of genes, enzymes, gene clusters, and proteins

F. velutipes

Ethanol production

58 potential enzymes associated with ethanol production were identified

[132]

H. erinaceus

•Lignocellulose degradation

•Biosynthesis of bioactive secondary metabolites

341 carbohydrate-active enzymes related to lignocellulose degradation, 447 transcription factors, and gene clusters contributing to bioactive secondary metabolites biosynthesis were identified

[133]

G. lucidum

•Terpenoid synthesis

•Triterpene biosynthesis

•Wood degradation

Numerous ligninolytic and carbohydrate-active enzymes, as well as the enzymes of the ganoderic acid biosynthetic pathway were determined

[136,137]

P. eryngii

Degradation of lignocellulose

Insights into CAZymes and oxidoreductases was provided

[144]

Discovering/establishing microsatellite markers databases

H. erinaceus

Genome-wide microsatellites

A comprehensive microsatellite markers database was established

[133]

Ganoderma boninense

The biology of G.boninense and its diversity

Novel polymorphic microsatellite markers were discovered and established

[147]

Uncovering the evolutionary aspects

Laetiporus sulphureus

Lignocellulose breakdown

The evolutionary history and roots of the enzymatic toolbox were refined

[142]

Coprinopsis cinerea (Coprinus cinereus)

Evolution of multicellular fungi

Rates of meiotic recombination were indicated to be low in the parts of the genome that remained unchanged over evolutionary time

[145]

Fistulina hepatica

New wood decomposition mechanisms in Agaricales

Changing its lifestyle to a brown-rot lifestyle may be a continuous procedure in this mushroom

[146]

Improving cultivation

L. edodes

Cultivation conditions

A rationale for partially replacing wood sawdust with agricultural wastes in cultivation was offered

[143]

Improving the knowledge about the biological properties

V. volvacea

Degradation of the cultivating compost containing agricultural waste

The knowledge about the biological properties associated with the degradation of the mentioned cultivating compost was improved

[38]

F. velutipes

Lignocellulose degradation

The high capacity of this mushroom for lignocellulose degradation was revealed

[132]

L. rhinocerotis

Medicinal properties

Information about the genetic basis of medicinal properties was provided

[135]

Providing predictive platforms

Omphalotus olearius

Sesquiterpenoid natural products

A prognosticative framework in Basidiomycota for obtaining sesquiterpenoid natural products was offered

[148]

L. rhinocerotis

Secondary metabolite biosynthesis

A platform for the identification of putative bioactive proteins and enzymes contributing to secondary metabolite biosynthesis was provided

[135]