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Australia: The Land Where Time Began |
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Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of
Land Plants Indicated by Phylogenomic Analyses
Fungi, which are decomposers, are key organisms in the recycling of
plant material in global carbon cycles. It was hypothesised by Chang et
al. that genomes of early
diverging fungi may have inherited from an ancestral species pectinases
that had been able to extract nutrients from land pants that contained
pectin and their algal allies (Streptophytes).
This study was aimed at inferring the geological timing of the
plant-fungus association, based on pectinase gene expansions and on the
organismal phylogeny. In this study 40 fungal genomes were studied, 3 of
which, including
Gonapodya prolifera,
were sequenced.
Rozella diverged first
from all other fungi, according to the organismal phylogeny from 136
housekeeping loci.
Gonapodya was included
among the flagellated fungal species that were predominantly aquatic in
the Chytridiomycota. A sister group to the Chytridiomycota were the
zygomycota I and zygomycota II, that were predominantly terrestrial
fungi, as well as the ascomycetes and basidiomycetes that comprise
Dikarya. There are 27 genes in the genome of
Gonapodya, which
represented 5 of the 7 classes of pectin-specific enzymes that are known
from fungi. A common ancestry is shared by most of these with pectinases
from Dikarya. Like many Dikarya
Gonapodya can use pectin
as a carbon source for growth in a pure culture, which indicates
functional and sequence similarity. Evidence that even ancient aquatic
fungi had adapted to extract nutrients from the plants in the green
lineage is provided by shared pectinases of Dikarya and
Gonapodya. It is implied
by this that 750 Ma (million years ago) the estimated maximum age of
origin of the Streptophytes, which contained pectin, represents a
maximum age for the divergence Chytridiomycota from the lineage that
included the Dikarya.
The majority of modern fungi are characterised by close associations
with plants or plant products. Fungi in Dikarya (Ascomycota and
Basidiomycota) have key roles as decomposers (Floudas et
al., 2012). Contrasting with
the Dikarya, the lineages that diverged early in the evolution of the
fungi, such as the zoosporic chytrids and some of the zygomycetes, use
diverse sources of nutrition (Stajich et
al., 2009). Many are
associated with animals or animal products, though there are some that
are associated with plants. Among early lineages the diversity of
nutritional modes raises the questions of what the ancestral food of
fungi might have been, and when the origin of the close and ecologically
vital association between plants and fungi may have occurred (James et
al., 2006; Sprockett et
al., 2011).
The questions about the ancestral nutrition of fungi were approached by
Chang et al. through analysis
of the fungal digestive enzyme genes, which break down plant material.
Studies of fungal degradation of plant material have traditionally been
focused on the breakdown of cellulose and lignin. However, cellulose is
distributed too widely across organisms that include green, red and
brown algae (Popper et al.,
2011) for cellulases to be used as good markers for the association with
the lineage of land plants. The earliest land plants had not lignin in
their structure (Popper et al.,
2011); therefore enzymes for degrading lignin may not have been present
in the ancestral fungi to break down plant material (Floudas et
al., 2012). On the other hand
pectins are polysaccharides that are present only in the cell walls of
the streptophyte algae (Sřrensen et
al., 2011; Wickett et
al., 2014). Pectin-specific
polysaccharides and the genes for their synthesis, more specifically,
have only been identified in the land plants and in “advanced”
streptophyte algae though not in the streptophyte algal species that
diverged early (Sorensen et al.,
2011; Mikkelsen et al.,
2014). Enzymes that are present in fungi that degrade multiple pectic
molecules are potentially good indicators of the association between
fungi and the land plant lineage.
In contrast with lignin and cellulose, pectins are water-soluble and
form a jelly-like matrix in the primary cell walls of plants. Pectins
are complex polymers often with poly- or oligosaccharide (e.g.,
aribogalactan, b-1, 4 galactan) side chains decorating backbones of
homogalactuonan, xylogalacturonan, rhamnogalacturonan,
rhamnogalacturonan I, and rhamnogalacturonan II. Multiple enzymes from
different families are required of glycoside hydrolases (GHs),
polysaccharide lyases (PL), and carbohydrate esterases (CE) (van den
Brink & de Vries, 2011; Benoit et
al., 2012). There are at least 9 families among the pectinases that
are pectin specific, including 3 GH families (GH28, GH53 & GH93), 4
polysaccharide lyase families (PL1, PL3, PL4 and PL11), and 2
carbohydrate esterase families CE8 and CE13). An important role is
played by enzymes from GH28 in the degradation of pectin backbones by
fungi (van der Brink & de Vries, 2011). The other nonpectin-specific
families, which may also breakdown other molecules include (GH2, GH35,
GH43, GH51, GH54, GH78, GH88, GH105, PL9, CE12, and CE1. In this study,
Chang et al. first surveyed
the distribution of families of pectinase genes across fungi and
outgroups. They then reconstructed pectinase phylogenies for a detailed
picture of the diversification of fungi during through the evolution of
major fungal lineages.
The goal of Chang et al. was
to reconcile periods when there was expansion of pectinase genes with
the fungal organismal phylogeny in order to identify times when
ancestral fungi were adapting to using plants for acquiring nutrients.
Chang et al. predicted that
if the ancestral fungal species were associated with land plants and the
charophytes that contained pectin the ancestral fungal species would
have contained at least some pectinases. The pectinases may not have
diversified until more recent cladogenesis and the rise of the Dikarya,
if the early fungi fed on animal or animal-like material, and only later
became associated with plants.
Chang et al. needed a robust
fungal phylogeny in order to infer patterns of pectinase evolution among
fungi. The branching order for the earliest splits among fungi has
remained controversial, in spite of recent efforts at resolution (James
et al., 2006; Liu et
al., 2009; Ebersberger et
al., 2012).
A large number of fungal genomes have been sequenced and annotated in
recent years, which led to phylogenies that had increasingly rich
sampling of loci and taxa (Ma et
al., 2009; James et al.,
2013; Suga et al., 2013;
Tisserant et al., 2013). In
this study, Chang et al.,
initiated a whole genome sequencing of
Gonapodya prolifera,
Coemansia reversa and
Conidiobolus coronatus,
in collaborating with Joint Genome Institute. They sampled whole genome
data from 127 fungi, as well as 13 species from other eukaryotic groups,
with an emphasis on the taxa that represented early splits in fungi. In
order to explore factors that contributed to phylogenetic conflicts and
to phylogenetic resolution, they applied multiple analytic methods to
individual and concatenated genes.
With improved genomic and taxonomic sampling of fungi and related taxa,
and with the study of
fungal pectinases, the aim of this study was to:
1)
Improve understanding of higher level fungal phylogeny,
2)
Infer the origin and diversification pattern of pectinases among fungi,
and
3)
Infer the phylogenetic and geological age of plant/fungus associations,
based on patterns of pectinase gene expansion.
Resolving the early splits in fungal evolution
Chang et al. have contributed
to a picture that is well resolved of the divergence of early fungi with
new genome sequences of 3 fungi that diverged early. The results are
congruent with other studies that used whole genome sequences for taxa
they have in common. The early evolution of fungi took place among
zoosporic lineages that were predominantly aquatic, that are represented
by the extant genera
Cryptomycota, Chytridiomycota
and
Blastocladiomycota
(Ebersberger et al., 2012;
Torruella et al., 2012; James
et al., 2013). The arbuscular
mycorrhizal
Rhizophagus, among the
terrestrial fungi, which represents Glomeromycota, is a member of the
zygomycota I clade. This is consistent with the Tisserant et
al. (2013) analysis of
complete genome sequences, though it contradicts earlier studies that
were based partly or largely on ribosomal gene sequences showing
Glomeromycota to be a sister group of Dikarya.
According to Chang et al.
phylogenomics has proven to be useful in resolving some controversial
phylogenetic problems. Potential pitfalls remain, however, even with
genome-wide data (Fernández et al.,
2014). In order to test for one of these pitfalls conflict among
individual genes was looked for using the FcLM tests and AU tests. Low
information content in individual genes was revealed by FcLM tests and
AU analyses, instead of finding strong conflicting signals.
Equivocal support for competing topologies at the nodes of interest was
shown by almost all individual genes. The conflict among earlier studies
may be explained by the lack of information content per gene (James et
al., 2006: Sekimoto et
al., 2011; Ebersberger et
al., 2012). It is suggested
by this that further resolution of the deeper divergence will result
from additional sequencing of genomes of taxa that were diverging early.
The nature of these early splits may be maybe the reason for the lack of
information content per gene. In fungal evolution the earliest splits
occurred much further back in time than 500 Ma (Taylor & Barbee, 2006;
Stajich et al., 2009; Parfree
et al., 2011). Any
evolutionary signal may have eroded over time, and therefore became
difficult to recover. During early fungal evolution radiation events may
have been too rapid to allow enough substitutions to accumulate for
phylogenetic resolution (Sekimoto et
al., 2011; Ebersberger et
al., 2012). It was suggested
by the results of the Bayesian analysis of Chang et
al. that a short internode,
if not a real polytomy, is present between the first 2 splits in the
fungal tree though not at subsequent nodes. The lack of data for
resolving these relationships is also demonstrated by high fixation
points or lack of fixation for the earliest splits in RADICAL analysis.
Difficulty in resolving whether Dikarya is the sisters group to
zygomycota I, as well as the relationship between
Rhizophagus and
Mortierella is similarly
reflected in failure to reach fixation in RADICAL analyses. It was shown
by the experiments of Chang et al.
with alternative data matrices that the branching order of species that
were evolutionarily isolated of
Rozella, Allomyces, and
Catenaria was influenced
by gene sequences that were missing from 1 or more of these taxa. It is
not clear whether the loci that are missing from such taxa,
nevertheless, improve overall inferences about their relationships
(Lemmon et al., 2009; Wiens &
Tiu, 2012). Relatively few sites that are reliably aligned were
available even for genes that were present, which made it difficult to
associated substitutions with the short branches of those lineages that
were diverging early, as a result of the broad taxonomic sampling in
this study.
Evidence of pectinase gene expansion for geological age divergence of
fungi
An ancestral species of fungi that was taking advantage of nutrients
from streptophyte plants that contained pectin, was found by the
analysis of Chang et al. to
be pointing to the common ancestor of Chytridiomycota and the
terrestrial fungi that underwent at least 9 duplications of pectinase
genes. There are 4 or more duplications that mapped to the ancestor of
Pezizomycotina (Ascomycota), that are the only other concentration of
pectinase duplications that are inferred on internal fungal branches.
There are 3 fungus-specific clades in the GH28 gene tree that contain
members of both Chytridiomycota and Dikarya that received 89% or better
bootstrap support, is supported by their interpretation as clades of
orthologues. There are many extant chytrids that are associated with
streptophyte plants (Sparrow, 1960). Chang et
al. provide evidence of
shared pectinase function, beyond homology and the genes and proteins,
by showing that the chytrids
G. prolifera can use the
purified pectins rhamnogalacturonan I and polygalacturonic acid as
sources of carbon. The fossil record for the plant lineage is rich
compared with that of the fungi. Chang et
al. provide the first
estimate of a maximum age for the fungi by linking the evolution of the
fungi to Streptophytes. It is estimated that the streptophytes that
contain pectin are no older than 750 Ma (Douzery et
al., 2004; Zimmer et
al., 2007; Parfrey et
al., 2011), and therefore the
common ancestor of Chytridiomycota and Dikarya that degraded pectin is
no older than 750 Ma. The minimum age of origin of fungi and the major
terrestrial fungal groups has been placed
at more than 1 Ga (billion years ago) by past studies that had no
maximum age restraint (Heckman et
al., 2001; Hedges et al.,
2004; Padovan et al., 2005;
Parfree et al., 2011). The
very old ages for fungi are inconsistent with the notion that the
diversification of plants and terrestrial fungi were interdependent on
each other, as well a being inconsistent with the age of plants that
contain pectin (Lücking et al.,
2009).
Plants that are homologous to pectinases predate the origin of pectin,
as is clear from the gene trees. It is suggested by reconstructions that
at least 5 copies of the GH28 family were already present in the common
ancestor of plants, Chromalveolata, and fungi. There are copies from 6
families in the oomycete Phytophthora, and the high copy numbers in each
family trace back to recent gene duplications following its divergence
from
Saprolegnia. The
distribution of pectinases across disparate eukaryotes could have
resulted from horizontal transfer from plants or fungi to other
organisms, as has been suggested by other genes for enzymes that were
secreted (Richards et al.,
2011). In restructuring the gene tree it could also reflect phylogenetic
error (though the methods used by Chang et
al. were conservative), or it
could be a reflection of diversity of ancestral genes with other
specificities that were co-opted for the breakdown of pectin.
Pectinases that evolve rapidly and have been repeatedly lost from fungi
that switched from nutrition based on plants. All or nearly all of the
pectinases were lost by yeasts (Saccharomyces
and
Shizosaccharomyces) as
they adopted nutrition form simple sugars. Pectinases were lost from
several fungal lineages when they associated with animals; examples
include species of the chytrid
Bathtrachochytrium, which
is parasitic on frogs,
Malassezia, the cause of
dandruff, and of inhabitants of mucous membranes,
Candida.
Similarly, it appears that pectinases have duplicated rapidly in
organisms that adopt nutrition that is plant-based. It is indicated by
the analysis of Chang et al.
that zygomycetes ancestors lost nearly all of the pectinase homologues.
Though there are no pectin-specific pectinases in
Rhizophagus irregularis
the high numbers of pectinase copies and low gene diversity of the major
pectinase family GH28 in
Phycomyces, Rhizopus, and
Mucor represent recent
gene duplications, which is consistent with previous findings (Mertens
et al., 2008).
Microbial slime and origin of terrestrial fungi
Fungi, which are decomposers, are key organisms in the recycling of
plant material in global carbon cycles. It was hypothesised by Chang et
al. that genomes of early
diverging fungi may have inherited from an ancestral species pectinases
that had been able to extract nutrients from land pants that contained
pectin and their algal allies (Streptophytes).
This study was aimed at inferring the geological timing of the
plant-fungus association, based on pectinase gene expansions and on the
organismal phylogeny. In this study 40 fungal genomes were studied, 3 of
which, including
Gonapodya prolifera,
were sequenced.
Rozella diverged first
from all other fungi, according to the organismal phylogeny from 136
housekeeping loci.
Gonapodya was included
among the flagellated fungal species that were predominantly aquatic in
the Chytridiomycota. A sister group to the Chytridiomycota were the
zygomycota I and zygomycota II, that were predominantly terrestrial
fungi, as well as the ascomycetes and basidiomycetes that comprise
Dikarya. There are 27 genes in the genome of
Gonapodya, which
represented 5 of the 7 classes of pectin-specific enzymes that are known
from fungi. A common ancestry is shared by most of these with pectinases
from Dikarya. Like many Dikarya,
Gonapodya can use pectin
as a carbon source for growth in a pure culture, which indicates
functional and sequence similarity. Evidence that even ancient aquatic
fungi had adapted to extract nutrients from the plants in the green
lineage is provided by shared pectinases of Dikarya and
Gonapodya. It is implied
by this that 750 Ma (million years ago) the estimated maximum age of
origin of the Streptophytes, which contained pectin, represents a
maximum age for the divergence Chytridiomycota from the lineage that
included the Dikarya.
The majority of modern fungi are characterised by close associations
with plants or plant products. Fungi in Dikarya (Ascomycota and
Basidiomycota) have key roles as decomposers (Floudas et
al., 2012). Contrasting with
the Dikarya, the lineages that diverged early in the evolution of the
fungi, such as the zoosporic chytrids and some of the zygomycetes, use
diverse sources of nutrition (Stajich et
al., 2009). Many are
associated with animals or animal products, though there are some that
are associated with plants. Among early lineages the diversity of
nutritional modes raises the questions of what the ancestral food of
fungi might have been, and when the origin of the close and ecologically
vital association between plants and fungi may have occurred (James et
al., 2006; Sprockett et
al., 2011).
The questions about the ancestral nutrition of fungi were approached by
Chang et al. through analysis
of the fungal digestive enzyme genes, which break down plant material.
Studies of fungal degradation of plant material have traditionally been
focused on the breakdown of cellulose and lignin. However, cellulose is
distributed too widely across organisms that include green, red and
brown algae (Popper et al.,
2011) for cellulases to be used as good markers for the association with
the lineage of land plants. The earliest land plants had no lignin in
their structure (Popper et al.,
2011), therefore enzymes for degrading lignin may not have been present
in the ancestral fungi to break down plant material (Floudas et
al., 2012). On the other hand
pectins are polysaccharides that are present only in the cell walls of
the streptophyte algae (Sřrensen et
al., 2011; Wickett et
al., 2014). Pectin-specific
polysaccharides and the genes for their synthesis, more specifically,
have only been identified in the land plants and in “advanced”
streptophyte algae though not in the streptophyte algal species that
diverged early (Sorensen et al.,
2011; Mikkelsen et al.,
2014). Enzymes that are present in fungi that degrade multiple pectic
molecules are potentially good indicators of the association between
fungi and the land plant lineage.
In contrast to Lignin and cellulose, pectins are water-soluble and form
a jelly-like matrix in the primary cell walls of plants. Pectins are
complex polymers often with poly- or oligosaccharide (e.g.,
aribogalactan, b-1, 4 galactan) side chains decorating backbones of
homogalactuonan, xylogalacturonan, rhamnogalacturonan,
rhamnogalacturonan I, and rhamnogalacturonan II. Multiple enzymes from
different families of glycoside hydrolases (GHs), polysaccharide lyases
(PL), and carbohydrate esterases (CE) are required for the complete
degradation of the pectin complex (van den Brink & de Vries, 2011;
Benoit et al., 2012). At
least 9 families among the pectinases are pectin specific, including 3
GH families (GH28, GH53 & GH93), 4 polysaccharide lyase families (PL1,
PL3, PL4 and PL11), and 2 carbohydrate esterase families CE8 and CE13).
An important role is played by enzymes from GH28 in the degradation of
pectin backbones by fungi (van der Brink & de Vries, 2011). The other
nonpectin-specific families, which may also breakdown other molecules,
include (GH2, GH35, GH43, GH51, GH54, GH78, GH88, GH105, PL9, CE12, and
CE1. In this study, Chang et al.
first surveyed the distribution of families of pectinase genes across
fungi and outgroups. They then reconstructed pectinase phylogenies for a
detailed picture of the diversification of fungi during the evolution of
major fungal lineages.
The goal of Chang et al. was
to reconcile periods when there was expansion of pectinase genes with
the fungal organismal phylogeny in order to identify times when
ancestral fungi were adapting to using plants for acquiring nutrients.
Chang et al. predicted that
if the ancestral fungal species were associated with land plants and the
charophytes that contained pectin the ancestral fungal species would
have contained at least some pectinases. The pectinases may not have
diversified until more recent cladogenesis and the rise of the Dikarya,
if the early fungi fed on animal or animal-like material, and only later
became associated with plants.
Chang et al. needed a robust
fungal phylogeny in order to infer patterns of pectinase evolution among
fungi. The branching order for the earliest splits among fungi has
remained controversial, in spite of recent efforts at resolution (James
et al., 2006; Liu et
al., 2009; Ebersberger et
al., 2012).
A large number of fungal genomes have been sequenced and annotated in
recent years, which led to phylogenies that had increasingly rich
sampling of loci and taxa (Ma et
al., 2009; James et al.,
2013; Suga et al., 2013;
Tisserant et al., 2013). In
this study, Chang et al.,
initiated a whole genome sequencing of
Gonapodya prolifera,
Coemansia reversa and
Conidiobolus coronatus,
in collaboration with Joint Genome Institute. They sampled whole genome
data from 127 fungi, as well as 13 species from other eukaryotic groups,
with an emphasis on the taxa that represented early splits in fungi. In
order to explore factors that contributed to phylogenetic conflicts and
to phylogenetic resolution, they applied multiple analytic methods to
individual and concatenated genes.
With improved genomic and taxonomic sampling of fungi and related taxa,
and with the study of
fungal pectinases, the aim of this study was to:
1)
Improve understanding of higher level fungal phylogeny,
2)
Infer the origin and diversification pattern of pectinases among fungi,
and
3)
Infer the phylogenetic and geological age of plant/fungus associations,
based on patterns of pectinase gene expansion.
Conclusions
It was shown by Change et al.
by using a robust phylogeny that pectinases, enzymes for degrading plant
cell walls, duplicated in an ancestral fungus that probably still lived
in freshwater, in association with streptophyte algae that contained
pectin. Using the age estimate of the streptophytes as a constant, the
age estimate of the common ancestor of terrestrial fungi predates the
origin of land plants. Early terrestrial fungi
may have evolved in
semiaquatic microbial slime, with the ancestors of zygomycetes tracking
arthropods or other animals, while the ancestors of Dikarya followed
plants onto land. The evidence from the results of this study for an
association of early fungi with early plants implicates fungi in
processes of decomposition and symbiosis in the earliest terrestrial
ecosystems.
Chang, Y., et al. (2015). "Phylogenomic Analyses Indicate that Early
Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants."
Genome Biology and Evolution 7(6): 1590-1601.
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Author: M.H.Monroe Email: admin@austhrutime.com Sources & Further reading |