posable elements which are affected by repeatinduced point mutation (RIP), a fungal-specific
genome defense mechanism against repetitive
sequences (Selker 1990; Soyer et al. 2014). RIP
can affect neighboring sequences (Gladyshev
and Kleckner 2017), and therefore genes
located within the AT isochores are subject to
increased mutation rates (Rouxel et al. 2011).
Among the genes located within the AT isochores, many encode effectors—small secreted
proteins that manipulate the host defense
(Jones and Dangl 2006; Lo Presti et al. 2015)—
and their location within these AT isochores
could promote rapid sequence diversification
of these genes.
Genome comparison between Fusarium
oxysporum f. sp. lycopersici strain Fol4287 and
Fusarium verticillioides showed that Fol4287
contains chromosomes 3, 6, 14, and 15 and
parts of the chromosomes 1 and 2 which do
not have syntenic chromosomes/regions in F.
verticillioides (Ma et al. 2010). These accessory
chromosomes and regions of chromosomes are
called lineage-specific in this tomato pathogen.
Again, the lineage-specific regions are rich in
transposons; show a lower gene density, a
higher proportion of unique genes, and a different codon usage; and may have a distinct
phylogenetic history compared the essential
chromosomes (Ma et al. 2010). In several additional fungal species, accessory chromosomes
have been described. These include the plant
pathogens Magnaporthe oryzae (Chuma et al.
2011; Dean et al. 2005), Cochliobolus carbonum
(Ahn and Walton 1996), Colletotrichum gloeosporioides (He et al. 1998; Masel et al. 1993),
Gibberella fujikuroi, and several host-specific
lineages of Alternaria alternata (Akamatsu
et al. 1999; Hatta et al. 2002; Hu et al. 2012;
Johnson et al. 2001). Recently, an accessory
chromosome has also been described in Botrytis cinerea (Van Kan et al. 2017). It is striking
that accessory chromosomes have been found
mostly in plant pathogenic fungi. One exception is the insect pathogenic fungus Metarhizium anisopliae, which harbors a single
accessory chromosome (Wang et al. 2003) and
is used as a biocontrol agent (Schrank and
Vainstein 2010).
In conclusion, the accessory chromosomes
in fungi show characteristics similar to accessory chromosomes found in other organisms as
they are enriched in repetitive elements, are
mainly heterochromatic, and often show a different GC content and codon usage compared
to the core chromosomes. However, these characteristics are not exclusive and thus do not
allow unequivocal identification of accessory
chromosomes because sequences with similar
characteristics can also be found within essential core chromosomes (Mo ¨ller and Stukenbrock 2017).
III. Fungal Accessory Chromosomes
Are Generally Associated with
Function
The dispensability of accessory chromosomes
for growth and development raises questions
on their functional role. B chromosomes in
plants and animals are mostly heterochromatic,
and therefore gene expression has been
assumed to be absent or repressed (BanaeiMoghaddam et al. 2013). Recent studies, however, report active transcription of coding
sequences located on a number of plant and
animal B chromosomes, indicating a functional
role of genes encoded on these chromosomes
(Banaei-Moghaddam et al. 2013; Carchilan et al.
2007; Graphodatsky et al. 2005; Ma et al. 2017;
Pereira et al. 2017; Ramos et al. 2017; Trifonov
et al. 2013; Yoshida et al. 2011). However, transcription is in general found to be lower compared to genes located on the core
chromosomes (Banaei-Moghaddam et al.
2015). To date, a fitness benefit of individuals
carrying B chromosomes has only been
reported for a small number of plant and animal species (Jones 1995; Yoshida et al. 2011).
One of these few cases is the exemplary rye B
chromosome, which protects meiocytes against
heat stress-induced damage (Pereira et al.
2017).
In contrast, genes located on fungal accessory chromosomes are often associated with a
function (see Table 2.1 and references therein).
30
M. Habig and E. H. Stukenbrock
genome defense mechanism against repetitive
sequences (Selker 1990; Soyer et al. 2014). RIP
can affect neighboring sequences (Gladyshev
and Kleckner 2017), and therefore genes
located within the AT isochores are subject to
increased mutation rates (Rouxel et al. 2011).
Among the genes located within the AT isochores, many encode effectors—small secreted
proteins that manipulate the host defense
(Jones and Dangl 2006; Lo Presti et al. 2015)—
and their location within these AT isochores
could promote rapid sequence diversification
of these genes.
Genome comparison between Fusarium
oxysporum f. sp. lycopersici strain Fol4287 and
Fusarium verticillioides showed that Fol4287
contains chromosomes 3, 6, 14, and 15 and
parts of the chromosomes 1 and 2 which do
not have syntenic chromosomes/regions in F.
verticillioides (Ma et al. 2010). These accessory
chromosomes and regions of chromosomes are
called lineage-specific in this tomato pathogen.
Again, the lineage-specific regions are rich in
transposons; show a lower gene density, a
higher proportion of unique genes, and a different codon usage; and may have a distinct
phylogenetic history compared the essential
chromosomes (Ma et al. 2010). In several additional fungal species, accessory chromosomes
have been described. These include the plant
pathogens Magnaporthe oryzae (Chuma et al.
2011; Dean et al. 2005), Cochliobolus carbonum
(Ahn and Walton 1996), Colletotrichum gloeosporioides (He et al. 1998; Masel et al. 1993),
Gibberella fujikuroi, and several host-specific
lineages of Alternaria alternata (Akamatsu
et al. 1999; Hatta et al. 2002; Hu et al. 2012;
Johnson et al. 2001). Recently, an accessory
chromosome has also been described in Botrytis cinerea (Van Kan et al. 2017). It is striking
that accessory chromosomes have been found
mostly in plant pathogenic fungi. One exception is the insect pathogenic fungus Metarhizium anisopliae, which harbors a single
accessory chromosome (Wang et al. 2003) and
is used as a biocontrol agent (Schrank and
Vainstein 2010).
In conclusion, the accessory chromosomes
in fungi show characteristics similar to accessory chromosomes found in other organisms as
they are enriched in repetitive elements, are
mainly heterochromatic, and often show a different GC content and codon usage compared
to the core chromosomes. However, these characteristics are not exclusive and thus do not
allow unequivocal identification of accessory
chromosomes because sequences with similar
characteristics can also be found within essential core chromosomes (Mo ¨ller and Stukenbrock 2017).
III. Fungal Accessory Chromosomes
Are Generally Associated with
Function
The dispensability of accessory chromosomes
for growth and development raises questions
on their functional role. B chromosomes in
plants and animals are mostly heterochromatic,
and therefore gene expression has been
assumed to be absent or repressed (BanaeiMoghaddam et al. 2013). Recent studies, however, report active transcription of coding
sequences located on a number of plant and
animal B chromosomes, indicating a functional
role of genes encoded on these chromosomes
(Banaei-Moghaddam et al. 2013; Carchilan et al.
2007; Graphodatsky et al. 2005; Ma et al. 2017;
Pereira et al. 2017; Ramos et al. 2017; Trifonov
et al. 2013; Yoshida et al. 2011). However, transcription is in general found to be lower compared to genes located on the core
chromosomes (Banaei-Moghaddam et al.
2015). To date, a fitness benefit of individuals
carrying B chromosomes has only been
reported for a small number of plant and animal species (Jones 1995; Yoshida et al. 2011).
One of these few cases is the exemplary rye B
chromosome, which protects meiocytes against
heat stress-induced damage (Pereira et al.
2017).
In contrast, genes located on fungal accessory chromosomes are often associated with a
function (see Table 2.1 and references therein).
30
M. Habig and E. H. Stukenbrock