Mucoromycota divergence (Bonfante and
Desiro ` 2017).
On the basis of the current data, Glomeromycotina can therefore be defined as a stable
component of the plant microbiota, since they
are found in most of the environments so far
investigated (Davison et al. 2015, 2018), but on
the other hand, they also host their own microbiota, given by the intracellular endobacteria as
well as by the bacteria which are commonly
associated to the surface of their extraradical
hyphae (Turrini et al. 2018).
Interestingly, the molecular investigations,
including the exploitation of transcriptomics
data, have also allowed the description of viral
sequences hosted within AM fungi (Turina
et al. 2018). Mycoviruses can therefore be considered an additional component of the AM
microbiome with the potential to influence the
biology of AM fungi and their host plant (Ikeda
et al. 2012).
III. Lessons from the Genome
Sequencing of AM Fungi
Our knowledge of the AM symbiosis mainly
mirrors a plant-centric view. This is due to (1)
the obligate biotrophic status of Glomeromycotina, which cannot be cultivated in the absence
of their host plants; (2) their multinuclear condition, i.e., hundreds of nuclei coexist within
one continuous cytoplasm; and (3) the absence
of observable sexual reproduction and a uninucleated life stage (Chen et al. 2018). All these
aspects hamper the use of the classical genetic
tools which have, by contrast, allowed to study
model fungi like Neurospora or Aspergillus, or
their host plants which offer genetically tractable systems. In addition, protocols to obtain a
stable genetic transformation of AM fungi are
not yet available.
In the first decade of the new century, the
development of -omics approaches and the first
sequencing of an AM fungal genome have
offered novel groundbreaking insights in their
biology. However, achieving the first
sequenced genome of a Glomeromycotina,
Rhizophagus irregularis, was not an easy task
and required many years (Martin et al. 2004;
Tisserant et al. 2013). The strain DAOM-197198
was selected for several reasons: it had been
hypothesized to possess a very small genome;
it easily grows in association with root organ
cultures, producing a large amount of noncontaminated fungal material; and – as a last
key feature – it does not host endobacteria, thus
representing a potentially more amenable scenario. The sequence of its 153-Mb haploid
genome showed a repertoire of about 30,000
genes and revealed a low level of polymorphism
offering for the first time a reply to the crucial
question: do the nuclei of AM fungi possess
multiple, highly diverged genomes? The data
strongly suggested the inconsistency of such a
hypothesis, which was also elegantly refuted by
the whole sequence of isolated single nuclei
(Lin et al. 2014). Mating (MAT)-related genes
were found to be expanded, suggesting the existence of cryptic sex-related processes and
opening the possibility that a non-observable
mating does not mean absence of sex. Genomic
analyses of several R. irregularis isolates clearly
proved that some strains are homokaryotic
(containing genetically identical nuclei with
one putative MAT locus) while other strains
are dikaryotic (harboring two distinct nuclear
genotypes each with a different MAT locus;
Ropars et al. 2016; Corradi and Brachmann
2017). Moreover, Chen et al. (2018), following
the single-nucleus sequencing approach
(Fig. 7.1), demonstrated that nuclei with distinct genotypes in their MAT alleles can
undergo recombination, originating genetic
diversity. Despite evidence of recombination,
however, clonality still appears to be the prevalent mode of reproduction (Chen et al. 2018).
A. The Biotrophism of AM Fungi
The expectations of the researchers involved in
genome sequencing of Rhizophagus irregularis
were first focused on another crucial question:
why are AM fungi unculturable? At a first
glance, their obligate biotrophy was not
explained by genome erosion or any related
loss of metabolic complexity in central metabolism. Only later it was clear that AM fungi do
7 Genetics and Genomics Decipher Partner Biology in Arbuscular Mycorrhizas
145
Desiro ` 2017).
On the basis of the current data, Glomeromycotina can therefore be defined as a stable
component of the plant microbiota, since they
are found in most of the environments so far
investigated (Davison et al. 2015, 2018), but on
the other hand, they also host their own microbiota, given by the intracellular endobacteria as
well as by the bacteria which are commonly
associated to the surface of their extraradical
hyphae (Turrini et al. 2018).
Interestingly, the molecular investigations,
including the exploitation of transcriptomics
data, have also allowed the description of viral
sequences hosted within AM fungi (Turina
et al. 2018). Mycoviruses can therefore be considered an additional component of the AM
microbiome with the potential to influence the
biology of AM fungi and their host plant (Ikeda
et al. 2012).
III. Lessons from the Genome
Sequencing of AM Fungi
Our knowledge of the AM symbiosis mainly
mirrors a plant-centric view. This is due to (1)
the obligate biotrophic status of Glomeromycotina, which cannot be cultivated in the absence
of their host plants; (2) their multinuclear condition, i.e., hundreds of nuclei coexist within
one continuous cytoplasm; and (3) the absence
of observable sexual reproduction and a uninucleated life stage (Chen et al. 2018). All these
aspects hamper the use of the classical genetic
tools which have, by contrast, allowed to study
model fungi like Neurospora or Aspergillus, or
their host plants which offer genetically tractable systems. In addition, protocols to obtain a
stable genetic transformation of AM fungi are
not yet available.
In the first decade of the new century, the
development of -omics approaches and the first
sequencing of an AM fungal genome have
offered novel groundbreaking insights in their
biology. However, achieving the first
sequenced genome of a Glomeromycotina,
Rhizophagus irregularis, was not an easy task
and required many years (Martin et al. 2004;
Tisserant et al. 2013). The strain DAOM-197198
was selected for several reasons: it had been
hypothesized to possess a very small genome;
it easily grows in association with root organ
cultures, producing a large amount of noncontaminated fungal material; and – as a last
key feature – it does not host endobacteria, thus
representing a potentially more amenable scenario. The sequence of its 153-Mb haploid
genome showed a repertoire of about 30,000
genes and revealed a low level of polymorphism
offering for the first time a reply to the crucial
question: do the nuclei of AM fungi possess
multiple, highly diverged genomes? The data
strongly suggested the inconsistency of such a
hypothesis, which was also elegantly refuted by
the whole sequence of isolated single nuclei
(Lin et al. 2014). Mating (MAT)-related genes
were found to be expanded, suggesting the existence of cryptic sex-related processes and
opening the possibility that a non-observable
mating does not mean absence of sex. Genomic
analyses of several R. irregularis isolates clearly
proved that some strains are homokaryotic
(containing genetically identical nuclei with
one putative MAT locus) while other strains
are dikaryotic (harboring two distinct nuclear
genotypes each with a different MAT locus;
Ropars et al. 2016; Corradi and Brachmann
2017). Moreover, Chen et al. (2018), following
the single-nucleus sequencing approach
(Fig. 7.1), demonstrated that nuclei with distinct genotypes in their MAT alleles can
undergo recombination, originating genetic
diversity. Despite evidence of recombination,
however, clonality still appears to be the prevalent mode of reproduction (Chen et al. 2018).
A. The Biotrophism of AM Fungi
The expectations of the researchers involved in
genome sequencing of Rhizophagus irregularis
were first focused on another crucial question:
why are AM fungi unculturable? At a first
glance, their obligate biotrophy was not
explained by genome erosion or any related
loss of metabolic complexity in central metabolism. Only later it was clear that AM fungi do
7 Genetics and Genomics Decipher Partner Biology in Arbuscular Mycorrhizas
145