morphological analyses (Balestrini and Bonfante 2014).
The repertoire of R. irregularis genes has
therefore provided an excellent basis for understanding not only the fungal biology but also
the genetics mechanisms underlying the AM
symbiosis. The genomes of AM fungi which
have been recently sequenced thanks to the
impressive advances in DNA sequencing technologies have provided the opportunity to
develop comparative genomics analyses
(Morin et al. 2018; Venice et al. 2019). The
genome size of AM fungi can be very diverse,
ranging from about 150 Mb of Rhizophagus
species (Chen et al. 2018) to 600 Mb of G.
rosea and 784 Mb of G. margarita. The genome
expansion seems to be strictly correlated with
the presence of transposable elements (TE)
which, in the case of G. margarita, represent
more than 80% of the whole genome. Interestingly, also ectomycorrhizal fungi belonging to
the truffle groups and characterized by the production of hypogeous fruitbodies have genomes very large and rich in TE (Murat et al.
2018).
Differently from Glomeromycotina, the
ecological role of their sister group, Mucoromycotina, is much more enigmatic. In the order
Endogonales, the family Endogonaceae contains some ectomycorrhizal fungi producing
small hypogeous truffle-like fruitbodies (Fassi
et al. 1969; Yamamoto et al. 2017), while the
other family, Densosporaceae, groups fungi
that live associated to early-diverging plants
(Desiro ` et al. 2013; Rimington et al. 2015) as
well as the fine root endophytes (Orchard et al.
2017). Remarkably, the genome sequencing of
four Endogonaceae fungi (Chang et al. 2018)
has detected the symbiotic signatures already
identified in the other mycorrhizal fungi such
as large genome size, high repetitive DNA content, and low diversity of plant cell walldegrading enzymes but without elevated small
secreted proteins/secretome ratios. Notwithstanding the absence of fungi belonging to the
Archeosporaceae, all the genomes of these
mycorrhizal Mucoromycota fungi share similar
features. AM fungi, however, have some further
specific traits which well explain their unculturability (lipid auxotrophism), their TE abundance (TE burst), their high compatibility
with host plants (strong reduction of cell walldegrading CAZymes), and expansion of some
metabolic pathways (chitin synthesis and degradation) allowing therefore a fine-tuning of the
molecular dialogue with their host (Venice et al.
2019).
The genomes of D. epigea (Sun et al. 2018),
G. margarita (Venice et al. 2019), and Endogonales (Chen et al. 2018) also allowed to gain new
information on endobacteria living in their
cytoplasm. The genome sequence led to the
detection of Mollicutes-related endobacteria
(MREs) in D. epigea and in three of the four
sequenced Endogonaceae. Their genomes can
therefore be read as “metagenomes.” By contrast, G. margarita genome confirmed the presence
of
Candidatus
Glomeribacter
gigasporarum, which was already sequenced
(Ghignone et al. 2012). The presence of such
endobacteria, which have also been discovered
in the phylogenetically related Mortierellomycotina (Uehling et al. 2017), strongly suggests
that endobacteria may be an evolutionary
marker of Mucoromycota. The intimate contact
between bacteria and fungi may have favored
horizontal gene transfer (Torres-Corte ´s et al.
2015; Naito et al. 2015; Sun et al. 2018), potentially leading to an impact on the fungal biology
(Salvioli et al. 2016).
B. From Structure to Function
The genome sequencing of AM fungi has so far
provided relevant information concerning their
genome structure and evolution, even if data
from some more distantly related members,
such as Archeospora, would be essential to better define their ancient relationships. By contrast, functional genomics study of AM fungi is
still at its infancy. Many genes, and mostly
those expressed during the symbiotic phase,
are orphan genes (i.e., do not show similarities
with genes listed in databases), and the lack of
genetic transformation procedures further
hampers their characterization.
Following the studies on pathogenic interactions, attention has been given to the secretome, the pool of proteins characterized by the
7 Genetics and Genomics Decipher Partner Biology in Arbuscular Mycorrhizas
147
The repertoire of R. irregularis genes has
therefore provided an excellent basis for understanding not only the fungal biology but also
the genetics mechanisms underlying the AM
symbiosis. The genomes of AM fungi which
have been recently sequenced thanks to the
impressive advances in DNA sequencing technologies have provided the opportunity to
develop comparative genomics analyses
(Morin et al. 2018; Venice et al. 2019). The
genome size of AM fungi can be very diverse,
ranging from about 150 Mb of Rhizophagus
species (Chen et al. 2018) to 600 Mb of G.
rosea and 784 Mb of G. margarita. The genome
expansion seems to be strictly correlated with
the presence of transposable elements (TE)
which, in the case of G. margarita, represent
more than 80% of the whole genome. Interestingly, also ectomycorrhizal fungi belonging to
the truffle groups and characterized by the production of hypogeous fruitbodies have genomes very large and rich in TE (Murat et al.
2018).
Differently from Glomeromycotina, the
ecological role of their sister group, Mucoromycotina, is much more enigmatic. In the order
Endogonales, the family Endogonaceae contains some ectomycorrhizal fungi producing
small hypogeous truffle-like fruitbodies (Fassi
et al. 1969; Yamamoto et al. 2017), while the
other family, Densosporaceae, groups fungi
that live associated to early-diverging plants
(Desiro ` et al. 2013; Rimington et al. 2015) as
well as the fine root endophytes (Orchard et al.
2017). Remarkably, the genome sequencing of
four Endogonaceae fungi (Chang et al. 2018)
has detected the symbiotic signatures already
identified in the other mycorrhizal fungi such
as large genome size, high repetitive DNA content, and low diversity of plant cell walldegrading enzymes but without elevated small
secreted proteins/secretome ratios. Notwithstanding the absence of fungi belonging to the
Archeosporaceae, all the genomes of these
mycorrhizal Mucoromycota fungi share similar
features. AM fungi, however, have some further
specific traits which well explain their unculturability (lipid auxotrophism), their TE abundance (TE burst), their high compatibility
with host plants (strong reduction of cell walldegrading CAZymes), and expansion of some
metabolic pathways (chitin synthesis and degradation) allowing therefore a fine-tuning of the
molecular dialogue with their host (Venice et al.
2019).
The genomes of D. epigea (Sun et al. 2018),
G. margarita (Venice et al. 2019), and Endogonales (Chen et al. 2018) also allowed to gain new
information on endobacteria living in their
cytoplasm. The genome sequence led to the
detection of Mollicutes-related endobacteria
(MREs) in D. epigea and in three of the four
sequenced Endogonaceae. Their genomes can
therefore be read as “metagenomes.” By contrast, G. margarita genome confirmed the presence
of
Candidatus
Glomeribacter
gigasporarum, which was already sequenced
(Ghignone et al. 2012). The presence of such
endobacteria, which have also been discovered
in the phylogenetically related Mortierellomycotina (Uehling et al. 2017), strongly suggests
that endobacteria may be an evolutionary
marker of Mucoromycota. The intimate contact
between bacteria and fungi may have favored
horizontal gene transfer (Torres-Corte ´s et al.
2015; Naito et al. 2015; Sun et al. 2018), potentially leading to an impact on the fungal biology
(Salvioli et al. 2016).
B. From Structure to Function
The genome sequencing of AM fungi has so far
provided relevant information concerning their
genome structure and evolution, even if data
from some more distantly related members,
such as Archeospora, would be essential to better define their ancient relationships. By contrast, functional genomics study of AM fungi is
still at its infancy. Many genes, and mostly
those expressed during the symbiotic phase,
are orphan genes (i.e., do not show similarities
with genes listed in databases), and the lack of
genetic transformation procedures further
hampers their characterization.
Following the studies on pathogenic interactions, attention has been given to the secretome, the pool of proteins characterized by the
7 Genetics and Genomics Decipher Partner Biology in Arbuscular Mycorrhizas
147