The combined genome sequencing efforts
have resulted in a large catalog of putative
CAZymes, maintained in the CAZy database
(Lombard et al. 2014). Similar to how it was
described above for secondary metabolism,
this catalog can be screened using a highthroughput synthetic biology approach. Putatively interesting CAZymes can be expressed in
a production host, and the enzyme activity can
be assayed. This approach precludes the need
to grow the original host fungus.
C. Mushroom Development
Mushrooms are the sexual reproductive structures of fungi (predominantly) of the phylum
Basidiomycota or, more specifically, the class
Agaricomycetes (Ku ¨es and Liu 2000; Ku ¨es and
Navarro-Gonza ´lez 2015). Mushrooms are a
nutritious and sustainable food source for a
growing world population. They can be
cultivated on low-quality agricultural waste
streams (e.g., manure, saw dust or straw),
which they convert into high quality food. As
such, they contribute to a circular economy
(Grimm and Wo ¨sten 2018) and are interesting
from a biotechnology perspective. Examples of
edible mushrooms include the white button
mushroom (Agaricus bisporus), the oyster
mushroom (Pleurotus ostreatus), and shiitake
mushroom (Lentinula edodes).
Few mushroom-forming fungi are genetically accessible, but notable exceptions are Schizophyllum commune and Coprinopsis cinerea,
both of which have been used as model systems
for decades (Ku ¨es and Navarro-Gonza ´lez 2015).
This has resulted in the identification of structural proteins involved in mushroom development, such as hydrophobins (Wo ¨sten 2001),
as well as multiple developmental regulators
(Terashima et al. 2005; Ohm et al. 2011, 2013).
The number of available genomes of
mushroom-forming fungi has dramatically
increased in recent years, although it should
be noted that most mushroom-forming fungi
were sequenced due to their capacity to degrade
lignocellulose (Ohm et al. 2014). Comparative
genomics studies have given important new
insights into the phylogeny of mushroomforming fungi (Varga et al. 2019), showing
that morphological diversification occurred
especially in the Cretaceous and Paleocene.
Moreover, numerous novel gene families have
been identified that may be involved in mushroom development (Sipos et al. 2017; Krizsa ´n
et al. 2019; Alma ´si et al. 2019), based on their
conservation in mushroom-forming species as
well as their gene expression profile during
mushroom development. These genes are currently studied in more detail, which is facilitated by the recent development of CRISPR/
Cas9 genome editing tools (Sugano et al. 2017;
Vonk et al. 2019).
D. Plant Interactions
Many fungi interact with plants in one way or
another. This can be beneficial for the host
plant, for example, in the case of mycorrhizal
fungi that form a symbiosis with plant roots. In
contrast, fungal pathogens can be detrimental
to plant health. Both these fungal lifestyles are
important from a biotechnology perspective,
since they can strongly impact the yield of agricultural crops.
Although plant pathogens are found across
the fungal kingdom, many destructive pathogens belong to the phylum Ascomycota. Examples include various species of Fusarium and
Verticillium, which were early targets of
genome sequencing (Cuomo et al. 2007; Ma
et al. 2010; Klosterman et al. 2011). Comparative genome analysis allowed the reconstruction of gene evolution of pathogenesis-related
genes, which are generally called effector genes.
More recently all Verticillium species were
sequenced, and the subsequent analysis
revealed frequent chromosomal rearrangements as well as gene family losses. Moreover,
in these species only about 200–600 speciesspecific genes occurred, which are markedly
different from the conserved genes and are
likely candidates for host specificity (ShiKunne et al. 2018). The class Dothideomycetes
harbors many pathogens, including the wheat
pathogen Zymoseptoria tritici (formerly known
as Mycosphaerella graminicola), tomato pathogen Passalora fulva (formerly known as Clados214
R. A. Ohm
have resulted in a large catalog of putative
CAZymes, maintained in the CAZy database
(Lombard et al. 2014). Similar to how it was
described above for secondary metabolism,
this catalog can be screened using a highthroughput synthetic biology approach. Putatively interesting CAZymes can be expressed in
a production host, and the enzyme activity can
be assayed. This approach precludes the need
to grow the original host fungus.
C. Mushroom Development
Mushrooms are the sexual reproductive structures of fungi (predominantly) of the phylum
Basidiomycota or, more specifically, the class
Agaricomycetes (Ku ¨es and Liu 2000; Ku ¨es and
Navarro-Gonza ´lez 2015). Mushrooms are a
nutritious and sustainable food source for a
growing world population. They can be
cultivated on low-quality agricultural waste
streams (e.g., manure, saw dust or straw),
which they convert into high quality food. As
such, they contribute to a circular economy
(Grimm and Wo ¨sten 2018) and are interesting
from a biotechnology perspective. Examples of
edible mushrooms include the white button
mushroom (Agaricus bisporus), the oyster
mushroom (Pleurotus ostreatus), and shiitake
mushroom (Lentinula edodes).
Few mushroom-forming fungi are genetically accessible, but notable exceptions are Schizophyllum commune and Coprinopsis cinerea,
both of which have been used as model systems
for decades (Ku ¨es and Navarro-Gonza ´lez 2015).
This has resulted in the identification of structural proteins involved in mushroom development, such as hydrophobins (Wo ¨sten 2001),
as well as multiple developmental regulators
(Terashima et al. 2005; Ohm et al. 2011, 2013).
The number of available genomes of
mushroom-forming fungi has dramatically
increased in recent years, although it should
be noted that most mushroom-forming fungi
were sequenced due to their capacity to degrade
lignocellulose (Ohm et al. 2014). Comparative
genomics studies have given important new
insights into the phylogeny of mushroomforming fungi (Varga et al. 2019), showing
that morphological diversification occurred
especially in the Cretaceous and Paleocene.
Moreover, numerous novel gene families have
been identified that may be involved in mushroom development (Sipos et al. 2017; Krizsa ´n
et al. 2019; Alma ´si et al. 2019), based on their
conservation in mushroom-forming species as
well as their gene expression profile during
mushroom development. These genes are currently studied in more detail, which is facilitated by the recent development of CRISPR/
Cas9 genome editing tools (Sugano et al. 2017;
Vonk et al. 2019).
D. Plant Interactions
Many fungi interact with plants in one way or
another. This can be beneficial for the host
plant, for example, in the case of mycorrhizal
fungi that form a symbiosis with plant roots. In
contrast, fungal pathogens can be detrimental
to plant health. Both these fungal lifestyles are
important from a biotechnology perspective,
since they can strongly impact the yield of agricultural crops.
Although plant pathogens are found across
the fungal kingdom, many destructive pathogens belong to the phylum Ascomycota. Examples include various species of Fusarium and
Verticillium, which were early targets of
genome sequencing (Cuomo et al. 2007; Ma
et al. 2010; Klosterman et al. 2011). Comparative genome analysis allowed the reconstruction of gene evolution of pathogenesis-related
genes, which are generally called effector genes.
More recently all Verticillium species were
sequenced, and the subsequent analysis
revealed frequent chromosomal rearrangements as well as gene family losses. Moreover,
in these species only about 200–600 speciesspecific genes occurred, which are markedly
different from the conserved genes and are
likely candidates for host specificity (ShiKunne et al. 2018). The class Dothideomycetes
harbors many pathogens, including the wheat
pathogen Zymoseptoria tritici (formerly known
as Mycosphaerella graminicola), tomato pathogen Passalora fulva (formerly known as Clados214
R. A. Ohm