The Fungal Tree of Life: from
Molecular Systematics to
Genome-Scale Phylogenies
JOSEPH W. SPATAFORA,1 M. CATHERINE AIME,2 IGOR V. GRIGORIEV,3
FRANCIS MARTIN,4 JASON E. STAJICH,5 and MEREDITH BLACKWELL6
1
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331;
2
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907;
3
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; 4Institut National de la
Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes,
Laboratoire d’Excellence Recherches Avancés sur la Biologie de l’Arbre et les Ecosystèmes Forestiers (ARBRE),
Centre INRA-Lorraine, 54280 Champenoux, France; 5Department of Plant Pathology and Microbiology and
Institute for Integrative Genome Biology, University of California–Riverside, Riverside, CA 92521;
6
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 and
Department of Biological Sciences, University of South Carolina, Columbia, SC 29208
ABSTRACT The kingdom Fungi is one of the more diverse
clades of eukaryotes in terrestrial ecosystems, where they
provide numerous ecological services ranging from
decomposition of organic matter and nutrient cycling to
beneficial and antagonistic associations with plants and
animals. The evolutionary relationships of the kingdom
have represented some of the more recalcitrant problems
in systematics and phylogenetics. The advent of molecular
phylogenetics, and more recently phylogenomics, has greatly
advanced our understanding of the patterns and processes
associated with fungal evolution, however. In this article,
we review the major phyla, subphyla, and classes of the
kingdom Fungi and provide brief summaries of ecologies,
morphologies, and exemplar taxa. We also provide examples
of how molecular phylogenetics and evolutionary genomics
have advanced our understanding of fungal evolution
within each of the phyla and some of the major classes.
In the current classification we recognize 8 phyla, 12 subphyla,
and 46 classes within the kingdom. The ancestor of fungi
is inferred to be zoosporic, and zoosporic fungi comprise
three lineages that are paraphyletic to the remainder of fungi.
Fungi historically classified as zygomycetes do not form a
monophyletic group and are paraphyletic to Ascomycota
and Basidiomycota. Ascomycota and Basidiomycota are
each monophyletic and collectively form the subkingdom
Dikarya.
INTRODUCTION
In 1996 the genome of Saccharomyces cerevisiae was
published and marked the beginning of a new era in
fungal biology (1). Since then, rapid advancements in
both sequencing technologies and computational biology have resulted in the sequencing of genomes for more
than 800 species (e.g., http://genome.jgi.doe.gov/fungi/).
These genomes represent a windfall of data that are
informing evolutionary studies of fungi and the search
for biological solutions to alternative fuels, bioremediation, carbon sequestration, and sustainable agriculture
and forestry (2). Indeed, the marriage between genomics
Received: 6 June 2017, Accepted: 11 June 2017,
Published: 15 September 2017
Editors: Joseph Heitman, Department of Molecular Genetics and
Microbiology, Duke University Medical Center, Durham, NC 27710;
Timothy Y. James, Department of Ecology and Evolutionary Biology,
University of Michigan, Ann Arbor, MI 48109-1048
Citation: Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE,
Blackwell M. 2017. The fungal tree of life: from molecular
systematics to genome-scale phylogenies. Microbiol Spectrum 5(5):
FUNK-0053-2016. doi:10.1128/microbiolspec.FUNK-0053-2016.
Correspondence: Joseph W. Spatafora, spatafoj@oregonstate.edu
© 2017 American Society for Microbiology. All rights reserved.
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and phylogenetics occurred early, both in the use of
phylogenetic techniques to study genome evolution and
in the use of genome-scale data to infer evolutionary
relationships. In this article we will review the impact
of genomic-scale phylogenies, along with standard molecular phylogenies, on our understanding of the evolution of the fungal tree of life and the classification that
communicates it.
Genomic data provide the maximum amount of
discrete genetic information available for phylogenetic
analyses, and hundreds to thousands of genes have been
identified as useful phylogenetic markers (3). Markov
clustering algorithms have been proven powerful tools
to identify orthologous clusters of proteins that can be
filtered for single-copy clusters that are useful in phylogenetic analyses (4). This approach has transformed
phylogenetics by no longer requiring selection of an
a priori set of markers (e.g., rDNA, RPB2, etc.), but
rather promotes the mining of a data set of genomes
for the largest set of appropriate markers. Furthermore,
hidden Markov models have proven to be valuable tools
for identifying and retrieving these markers in newly
sequenced genomes and rapidly growing genome-scale
phylogenetic data sets (5).
The estimation of species trees from genome-scale
data sets is not without challenges, however. Phylogenetic analyses of genomic data have revealed that
different genes within a genome can have different evolutionary histories, i.e., phylogenetic conflict (6). Sources
of conflict include incomplete lineage sorting (or deep
coalescence), hybridization, and horizontal gene transfer, and the detection and characterization of this conflict in the context of phylogenetic inference are still in
their infancy (7). The application of standard measures
of topological support, such as the bootstrap partition,
can also be difficult to interpret, due to the observation
that nodes that resolve differently in different gene data
sets can have high or maximum bootstrap partition
values in a subset of analyses (e.g., 8, 9). At the time of
the writing of this manuscript the majority of genomescale phylogenetic analyses focus on the analysis of
concatenated superalignments, but development and use
of supertree methods, gene tree-species tree reconciliations, and alternative measures of nodal support are
increasing (e.g., 8, 10) and will be developed further over
the coming years.
Despite the challenges mentioned above, phylogenetic analyses of genome-scale data sets, and more
traditional multigene data sets, have greatly advanced
our understanding of fungal evolution. Historically,
the fungi were divided into more or less four groups—
chytridiomycetes, zygomycetes, ascomycetes, and
basidiomycetes—defined by morphological traits associated with reproduction. (Note: The suffix “-mycetes”
is used to denote a class-level taxonomic group in fungal
nomenclature, e.g., Agaricomycetes. Its use as a lowercase noun, however, signifies an informal name and
not an explicit taxonomic rank.) The chytridiomycetes,
or zoosporic fungi, were recognized based on their production of zoospores, characterized by a single posterior,
smooth flagellum. The zygomycetes were characterized
by gametangial conjugation and the production of
zygospores, coenocytic hyphae, and typically asexual
reproduction by sporangia. The ascomycetes and basidiomycetes were identified by the production of asci
and basidia, respectively, possession of regularly septate hyphae, and a dikaryotic nuclear phase in their
life cycle. The classification of the kingdom Fungi used
here recognizes eight phyla (Fig. 1, Table 1), with the
zoosporic fungi comprising the first three lineages of
the kingdom—Cryptomycota/Microsporidia, Chytridiomycota, and Blastocladiomycota—since the divergence
from the last universal common ancestor (LUCA) of
Fungi.
The resolution of zoosporic fungi as paraphyletic
rejects the flagellum as a diagnostic trait (synapomorphy) for a monophyletic group of flagellated fungi.
Rather, it is an ancestral (symplesiomorphic) trait inherited from the LUCA of the kingdom Fungi. Most
extant species of fungi are nonflagellated and are the
result of multiple losses of the flagellum during fungal
evolution. Two losses of the flagellum have occurred,
giving rise to the Microsporidia and the most recent
common ancestor (MRCA) of the remaining phyla of
zygomycetes, ascomycetes, and basidiomycetes. Inferences of additional losses of the flagellum are required
for the placement of nonflagellated species among the
Chytridiomycota (11) and possibly for the placement
of the enigmatic zoosporic genus Olpidium among
zygomycetes (12), but the absolute number of losses
is unclear. The zygomycetes are also paraphyletic and
are classified in two phyla: Zoopagomycota and Mucoromycota (13). This classification rejects the zygospore as a synapomorphy for the zygomycetes; rather,
it was inherited from the MRCA of terrestrial fungi
and lost in the MRCA of ascomycetes and basidiomycetes. The monophyly of ascomycetes and basidiomycetes has been confirmed, and they are classified as
the phyla Ascomycota and Basidiomycota, respectively,
of the subkingdom Dikarya (14). More information
on character evolution will be highlighted throughout
this article.
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The Fungal Tree of Life
FIGURE 1 Fungal tree of life. Cladogram of the kingdom Fungi based on published
multi-gene and genome-scale phylogenies (11–14, 17, 18, 32, 33, 83, 98, 109, 112, 167,
168). Polytomies represent regions of the tree currently unresolved by molecular and
genomic data.
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TABLE 1 Classification of the kingdom Fungi
Cryptomycota M.D.M. Jones & T.A. Richards 2011 [=Rozellomycota
Doweld (2011)]
Microsporidia
Blastocladiomycota T.Y. James (2007)
Blastocladiomycetes Doweld (2001)
Chytridiomycota Hibbett et al. (2007)
Chytridiomycetes Caval.-Sm. (1998)
Monoblepharidomycetes J.H Schaffner (1909)
Neocallimastigomycetes M.J. Powell (2007)
Zoopagomycota Gryganski et al. (2016)
Zoopagomycotina Benny (2007)
Kickxellomycotina Benny (2007)
Entomophthoromycotina Humber (2007)
Basidiobolomycetes Doweld (2001)
Neozygitomycetes Humber (2012)
Entomophthoromycetes Humber (2012)
Mucoromycota Doweld (2001)
Glomeromycotina Spatafora & Stajich (2016)
Glomeromycetes Caval.-Sm. (1998)
Mortierellomycotina Hoffm., K. Voigt & P.M. Kirk (2011)
Moretierellomycetes Caval.-Sm. (1998)
Mucoromycotina Benny (2007)
Ascomycota (Berk.) Caval.-Sm. (1998)
Pezizomycotina O.E. Erikss. & Winka (1997)
Arthoniomycetes O.E. Erikss. & Winka (1997)
Coniocybomycetes M. Prieto & Wedin (2013)
Dothideomycetes O.E. Erikss. & Winka (1997)
Eurotiomycetes O.E. Erikss. & Winka (1997)
Geoglossomycetes Zheng Wang, C.L. Schoch & Spatafora
(2009)
Laboulbeniomycetes Engler (1898)
Lecanoromycetes O.E. Erikss. & Winka (1997)
Leotiomycetes O.E. Erikss. & Winka (1997)
Lichinomycetes Reeb, Lutzoni & Cl. Roux (2004)
Orbiliomycetes O.E. Erikss. & Baral (2003)
Pezizomycetes O.E. Erikss. & Winka (1997)
Sordariomycetes O.E. Erikss. & Winka (1997)
Xylonomycetes Gazis & P. Chaverri (2012)
Saccharomycotina O.E. Erikss. & Winka (1997)
Saccharomycetes G. Winter (1880)
Taphrinomycotina O.E. Erikss. & Winka (1997)
Archaeorhizomycetes Rosling & T.Y. James (2011)
Neolectomycetes O.E. Erikss. & Winka (1997)
Pneumocystidomycetes O.E. Erikss. & Winka (1997)
Schizosaccharomycetes O.E. Erikss. & Winka (1997)
Taphrinomycetes O.E. Erikss. & Winka (1997)
Basidiomycota R.T. Moore (1980)
Agaricomycotina Doweld (2001)
Agaricomycetes Doweld (2001)
Dacrymycetes Doweld (2001)
Tremellomycetes Doweld (2001)
Wallemiomycetes Zalar, de Hoog & Schroers (2005)
Pucciniomycotina R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Agaricostilbomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Atractiellomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Classiculomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Cryptomycocolacomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Cystobasidiomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Microbotryomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
One of the greatest challenges in evolutionary biology
of fungi is accurately estimating geologic dates of the
origin of the kingdom Fungi, emergence of the major
phyla, and diversification of extant lineages (15). Our
knowledge of the fossil record of fungi is less than
that of plants and animals, but there does exist an increasing number of fossils that can be assigned to major
groups of fungi based on their morphological similarity to extant taxa (16). An important observation is
that morphologies associated with Blastocladiomycota,
Chytridiomycota, Mucoromycota, and Ascomycota are
present in the early Devonian and are associated with the
earliest known land plant flora of the Rhynie chert. This
observation, in combination with relaxed molecular
clock analyses (e.g., 17, 18), suggests that the common
ancestors of the phyla of Fungi are in fact old and may
have been among the first terrestrial organisms. The
interpretation of fungus-like fossils can be challenging,
however, as it is difficult to interpret some morphologies
that are not present among extant lineages as definitive
representatives of the kingdom Fungi (19).
In this article we will highlight the major phyla of
fungi based on the current understanding of the fungal
tree of life. In doing so, we will outline their phylogenetic
diversity and classification, provide examples of important taxa for each group, and discuss advancements
in our understanding of morphological and ecological
evolution through the analysis of genomic and molecular data. There are many specialized terms used in this
article, and we are unable to fully define all of them here.
However, Fig. 2 to 5 provide examples of taxa and
morphologies discussed herein, but the reader is directed
to more traditional textbooks in mycology for more
detailed discussions.
ZOOSPORIC FUNGI (FIG. 2)
Before we consider zoosporic fungi, a brief discussion
of some unique aspects of their development and morphology is necessary. The morphology of zoosporic
Mixiomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Pucciniomycetes R. Bauer, Begerow, J.P. Samp.,
M. Weiss & Oberw. (2006)
Tritirachiomycetes Aime & Schell (2011)
Ustilaginomycotina Doweld (2001)
Exobasidiomycetes Begerow, M. Stoll & R. Bauer 2007
Malasseziomycetes Denchev & T. Denchev 2014
Moniliellomycetes Q.M. Wang, F.Y. Bai & Boekhout (2014)
Ustilaginomycetes E. Warming (1884)
Incertae sedis
Entorrhizomycetes Begerow, Stoll & R. Bauer (2007)
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FIGURE 2 Examples of zoosporic fungal diversity. (a) Rozella allomycis (Cryptomycota)
parasitizing hyphae of Allomyces (Blastocladiomycota). Chytridiomycota: (b) C. hyalinus
(Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids; (c) Catenochytridium sp. (Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids;
(d) Monoblepharis polymorpha (Monoblepharidomycetes) mature zygote or oospore,
empty and mature antheridia and antherozoids or male gametes emerging from antheridium (by Marilyn M. N. Mollicone); (e) Neocallimastix sp. (Neocallimastigomycetes)
monocentric thallus with rhizoids (by Gary Easton); (f) Olpidium bornovanus (incertae
sedis) zoospores (photo by D’Ann Rochon); (g) Neocallimastix sp. (Neocallimastigomycetes) multiflagellate zoospores (photo by Gary Easton).
fungi varies depending on the extent of their thallus
development, number and position of reproductive
structures, and position in the substrate. Thalli may exist
as single cells with sparse rhizoidal systems to more
extensive networks of rhizoids (rhizomycelia) and mycelial thalli. Endobiotic chytrids are partially or completely immersed in their substrate, while only the
rhizoids of epibiotic chytrids are immersed. Often, the
thalli of single-celled chytrids are converted entirely to
thin-walled zoosporangia or thick-walled resting sporangia (holocarpic condition), and others have thalli that
are only partially converted to reproductive structures
(eucarpic condition). Other terms describe the number
of reproductive structures produced by an individual:
a single sporangium on a thallus is a monocentric thallus, and multiple sporangia on a rhizomycelium or mycelium are termed polycentric. Zoosporangia, in which
zoospores are produced, are asexual reproductive structures; resting sporangia that germinate by release of flagellated cells and resting spores that germinate by germ
tubes may be asexual or sexual structures.
Cryptomycota/Microsporidia
Cryptomycota plus Microsporidia are sister to the remaining lineages of Kingdom Fungi. (Note: Rozellomycota [20] is another name for Cryptomycota [21]
based on the genus Rozella and the principle of autotypification [14]. Cryptomyces is a genus in Ascomycota
and cannot be used to typify Cryptomycota.) Cryptomycota consists of a handful of described taxa and taxa
that are known only from environmental samples. One
described taxon is Rozella (Fig. 2a), a biotrophic intracellular parasite of other zoosporic fungi of Chytridiomycota and Blastocladiomycota and oomycetes of the
kingdom Stramenopila (22). There are few additional
described genera and species of Cryptomycota, but
environmental sampling using molecular markers has
revealed a phylogenetically diverse assemblage of fungi
detected in soils, marine and freshwater sediments, and
oxygen-depleted environments (23, 24). Some environmental Cryptomycota produce zoospores with a single,
smooth flagellum, but chitin, a cell wall carbohydrate
produced by most fungi, was not originally detected in
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the life history stages first observed (25). A more recent
study detected chitin restricted to the cyst phase that
attaches to the Allomyces hyphae and in the inner wall of
the resting sporangia (26). The ecology of the environmental Cryptomycota is largely conjecture at this time,
because they have not been cultured, an observation
frequently invoked in fungal systems to infer an obligate
biotroph. Recently, molecular data have determined
that Paramicrosporidium (20), nonflagellated parasites
of amoebae, and Amoeboaphelidium, an algal parasite,
are members of Cryptomycota (27), lending support to
parasitism as an ecological signature of the phylum.
Microsporidia are intracellular parasites of all major
groups of animals. They are particularly well known
from insects, crustaceans, and fish but are also known
to occur in mammals, including humans (28). Microsporidia produce unique spores that infect host cells
through a harpoon-like organelle that pierces the host
cell membrane and provides a conduit for the injection
of the parasite’s cytoplasm (29). Once inside the host
cell, a spore, which includes an inner chitin-containing
wall, is ultimately formed. The phylogenetic affinity of
Microsporidia has been difficult to determine, with past
classifications placing it among the polyphyletic protists,
and early multigene phylogenies placing it in different
parts of the kingdom Fungi (reviewed in reference 30).
Genome-scale phylogenies have also proven problematic
due to highly reduced genomes and fast rates of nucleotide substitution (31), but multiple analyses have garnered increasing support for its close relationship to
Cryptomycota (32, 33). Comparative genomic analyses
have demonstrated that both groups share genomic
traits including a nucleotide transporter that Microsporidia use for obtaining ATP from their hosts (33).
This phylogenetic placement of Microsporidia provides
further evidence for the early origins of parasitism and
more than one loss of the flagellum within the kingdom
Fungi.
Blastocladiomycota
The remaining two phyla of zoosporic fungi are Blastocladiomycota and Chytridiomycota. The branching
order of these two lineages is unresolved (Fig. 1), and
both have been inferred as the sister lineage to the
terrestrial, nonflagellated fungi in large multigene and
genome-scale phylogenetic analyses (11, 13, 18). The
failure to resolve this branching order appears to be attributed to low phylogenetic signal, rather than strong
conflict among competing individual gene trees (18),
although only two species of Blastocladiales have been
sequenced at this time. Resolution of this branching
is central to accurately understanding the changes in
life cycles and morphology, especially the loss of flagellum that accompanied the transition onto land. Additional taxon sampling and analysis of changes associated
with genome content (e.g., phylogenetic mapping of
gene birth events, rare genomic changes, etc.) will be
required.
Blastocladiomycota contains a single class and order,
Blastocladiomycetes and Blastocladiales, respectively.
Fossils of both sporothalli and gametothalli have been
described from the Lower Devonian (Rhynie chert) as
Paleoblastocladia (34), supporting it as an ancient lineage, but current molecular data are consistent with extant species sharing a recent MRCA as compared to
other phyla of fungi. Blastocladiomycota exhibit a range
of growth morphologies from monocentric with limited
thallus development to polycentric with the production
of robust, coenocytic hyphae. Furthermore, most known
species exhibit a true alternation of generation with
free-living haploid and diploid life stages. In Allomyces,
for example, free-living haploid thalli produce male and
female gametangia that can usually be differentiated
through color and size; the male gametangia are typically pigmented with carotenoids and are smaller in size
than female gametangia. Both male and female gametangia produce motile gametes (planogametes) that
fuse to form a diploid zygote, which germinates to form
a free-living diploid thallus. This thallus produces sporangia that yield diploid zoospores that are released
into the environment and germinate to form other diploid thalli. The diploid thallus ultimately matures and
produces resistant sporangia that are the sites of meiosis
and production of haploid zoospores, which when released into the environment germinate into haploid
thalli, completing the life cycle. Meiosis associated with
spore formation (sporic) is unknown in any other fungi.
Well-studied genera within Blastocladiales include
Allomyces, Blastocladiella, Coelomomyces, and Physoderma, which exhibit saprobic and parasitic ecologies
associated with animals and plants. Allomyces is frequently isolated from soil and serves as an excellent instructional model of polycentric development (mycelial
development with multiple sporangia) and alternation
of generations. Its ease of growth on synthetic media
with simple sugar sources is consistent with a saprobic
life history. Blastocladiella is another saprobic species
isolated from soil, but it displays monocentric development, with a simple thallus consisting of a single sporangium anchored to its substrate by rhizoidal elements.
Coelomomyces is a parasite of mosquitoes and copepods, with alternate generations produced in different
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hosts. Haploid zoospores infect copepods and produce
one- to two-celled wall-less hyphal bodies within the
host. These hyphal bodies give rise to flagellated gametes
that fuse inside or outside of the copepod host, resulting
in a diploid flagellated zygote that infects mosquito larvae. Inside the mosquito, the fungus develops a limited
diploid thallus that produces resting sporangia, which
are the site of meiosis and production of haploid zoospores. Physoderma includes stem and foliar pathogens
of plants (e.g., corn, alfalfa, etc.), which is relatively rare
for zoosporic species of the kingdom Fungi. Species of
Physoderma produce monocentric epibiotic sporangia
that infect a single host cell, but as the infection progresses, polycentric growth develops, producing large
endobiotic sporangia that occupy much of the host cell.
Chytridiomycota
Chytridiomycota includes three classes of fungi:
Chytridiomycetes, Monoblepharidomycetes, and Neocallimastigomycetes. Although some classifications recognize the latter two classes as phyla (e.g., 14), the three
taxa collectively form a well-supported monophyletic
clade in genome-scale analyses, but their relationship to
each other is uncertain (18). Chytridiomycota may have
been the earliest fungi in terrestrial environments, but it
is not clear if certain Precambrian microfossils actually
represent species of the phylum. Spherules and flaskshaped fossils from chert lenses of the Early Devonian
Rhynie chert formation have been interpreted as thalli
and zoosporangia of Chytridiomycota. The study of
plants and plant parts, including pollen, has been a productive means of discovering and identifying increasing
numbers of Chytridiomycota fossils and the presumptive
reactions of their hosts 412 million years ago (16).
Chytridiomycetes
Chytridiomycetes are water-inhabiting fungi, often
parasitic on algae and oomycetes, or soil inhabitants,
some of which are parasitic on vascular plants. A few
chytrids parasitize animal eggs and protozoa, while
others are saprobic on the decaying remains of plants.
Multigene phylogenetic analyses, new culture techniques, and additional collections of Chytridiomycetes
have revealed greater diversity and led to increased
numbers of orders in which to classify about 700 species in under 90 genera (e.g., 11, 14). Today there
are 10 described orders of Chytridiomycetes: Chytridiales, Spizellomycetales, Cladochytriales, Rhizophydiales,
Polychytriales, Rhizophlyctidales, Lobulomycetales, Synchytriales, Gromochytriales, and Mesochytriales (e.g.,
35–39).
An exemplar life cycle is that of Chytriomyces
hyalinus, which forms a well-developed rhizoidal system within its substrate (Fig. 2b). The sporangium that
develops from the encysted zoospore has a saucershaped operculum from which zoospores escape into a
fibrous vesicle of overlapping filaments where the cells
complete their maturation and then escape (40). The
zoospores encyst and germinate to form new sporangia
and rhizoids (asexual thalli) or to function as sexual
thalli. This is one of the few members of the Chytridiomycetes in which sexual reproduction has been well
documented. The rhizoids of the two thalli come into
contact and fuse, and a resting spore forms at the junction of the rhizoidal anastomosis. The resting sporangium develops a thick wall and eventually germinates
by production of zoospores, apparently after meiosis
(41). Other well-studied members of Chytridiomycetes
include Synchytrium endobioticum, a pathogen that
causes potato wart disease, and Nowakowskiella, an
operculate, polycentric genus of aquatic saprobes of
decaying plant materials. Species of Nowakowskiella
are often isolated from pond water by using cellulosic
baits. The most widely studied chytrid is Batrachochytrium dendrobatidis, the fungus associated with amphibian declines (42, 43). The disease was first detected
in Australia and Panama, but it now has been found on
all continents except Antarctica. Estimates predict that
30% of the world’s amphibian species will be affected by
severe population decline or extinction (44–47). Zoospores attack the keratinized parts of the amphibian,
such as larval mouthparts and the first two layers of
adult skin, to cause the infection. The flagella are resorbed, and the B. dendrobatidis cells enlarge within the
infected host cells. Growth of the somatic cells and their
conversion to zoosporangia cause the hyperplasia and
hyperkeratosis that are symptomatic of the disease. Severe infections reduce the efficiency of cutaneous respiration and osmoregulation. Evolutionary analyses of the
B. dendrobatidis genome revealed that it has evolved
from saprobic ancestors and that its unique ecology of
being a vertebrate pathogen is correlated with lineagespecific expansion of multiple gene families of proteases
(48).
Monoblepharidomycetes
Monoblepharidomycetes consists of only about 30 species in 6 genera, most of which are saprobes that
grow in fresh water on submerged twigs and fruits. The
fungi can be isolated by baiting soil samples in water
with hemp or sesame seeds. Genera are distinguished
in part by a polycentric mycelial thallus (Gonapodya,
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Monoblepharella, and Monoblepharis) or a uniaxial
thallus (Oedogoniomyces, Harpochytrium, and Hyaloraphidium). When hyphae are present in Monoblepharidales, they appear foamy or reticulate because the
protoplasm is highly vacuolated. Monoblepharidales is
of special interest because of its unique method of sexual
reproduction using a nonmotile female gametangium
and a flagellated male gamete, unlike any other fungus.
Monoblepharis polymorpha has a well-developed
branched thallus consisting of hyphae with a foamy appearance. Elongated zoosporangia are borne singly at
the hyphal tips subtended by a septum. Zoospores are
released from the tip of the sporangium, swim for a time,
become rounded, and germinate by a germ tube to form
a new mycelium. The same thallus that bears sporangia
also produces gametangia when subjected to higher
temperatures. The elongated male gametangium is borne
on the large, rounded egg-like female gametangium
(Fig. 2d). Uniflagellate gametes formed within the male
gametangium mature and are released. A single male
gamete fertilizes the enlarged female gamete, resulting in
cytoplasmic fusion and production of a diploid zygote.
The zygote functions as a resting spore and germinates
by producing a hypha to initiate a new thallus. The site
of meiosis has not been demonstrated but probably
occurs in early divisions of the zygote nucleus (49, 50).
Neocallimastigomycetes
The zoospores of members of Neocallimastigomycetes
were once considered to be flagellated protozoa, but
DNA sequences placed them in a distinct group of the
core chytrids (11). The class consists of about 20 species
placed in 6 genera, including Neocallimastix, Orpinomyces, and Piromyces (Fig. 2e). All species inhabit anaerobic regions of the rumen and hindgut of herbivores,
and they produce cellulases and xylanases that help to
degrade the dietary fibers from plant cell walls (51, 52).
Phylogenomic analyses revealed that many of these
plant cell wall-degrading enzymes are of bacterial origin
and represent a horizontal gene transfer from bacteria that presumably co-occur with Neocallimastigales
in the herbivore digestive tract (53). All species are
obligate anaerobes, and although a few other fungi (e.g.,
Blastocladia and certain yeasts in Saccharomycetales)
are facultatively anaerobic, among fungi only members of Neocallimastigales require completely anaerobic
environments. As a group, these fungi grow on a range
of simple and complex carbohydrates and exhibit
mixed acid fermentation (54), and renewed attention is
aimed at their potential in applied industrial mycology
(55).
ZYGOMYCETE FUNGI (FIG. 3)
As mentioned previously, genome-scale phylogenies do
not support the monophyly of zygomycetes and reject
the zygospore as a synapomorphy for them (13). Rather,
the zygospore is best interpreted as arising in the MRCA
of Zoopagomycota, Mucoromycota, Ascomycota, and
Basidiomycota and lost in the MRCA of Dikarya (Ascomycota + Basidiomycota). Most zygomycetes are characterized by coenocytic hyphae and sporangial asexual
reproduction, but lineages characterized by septate or
compartmentalized hyphae and/or asexual reproduction
by formation of conidia exist. Importantly, it is with the
emergence of the zygomycete fungi that we observe a
loss of the fungal flagellum and the rise of the terrestrial,
filamentous fungi. It is generally assumed that this loss of
the flagellum in the kingdom Fungi corresponds to the
transition to a terrestrial environment and the dawn of
early terrestrial ecosystems. As such, zygomycetes represent an important group of fungi for ecological studies
of host association and diversification of nutritional
modes and cell biology studies regarding the evolution of
centrosomes, organelles associated with hyphal growth
and differentiation, and multicellularity.
Zoopagomycota
Zoopagomycota is the sister to Mucoromycota+Dikarya.
It comprises three subphyla: Zoopagomycotina, Kickxellomycotina, and Entomophthoromycotina. The primary ecologies of members of the phylum include
pathogens and commensals of animals, parasites of other
fungi and amoebae, and rarely, as plant associates.
The phylogenetic placement of Zoopagomycota as sister
to the remainder of nonflagellated fungi is important for
numerous reasons, but two are highlighted here. First,
diversification with animals and nonplant hosts occurred
at least as early as diversification with terrestrial plants.
This suggests that fungi were among the first terrestrial
organisms and that fossils of the first land animals should
be examined with greater scrutiny for fungal associations, potentially providing a more complete picture of
early terrestrial fungi. Second, the loss of the flagellum
in fungi corresponds to other modifications, including
the loss of the centriole. Most nonflagellated fungi of
Mucoromycota, Basidiomycota, and Ascomycota possess an organelle unique to fungi, the spindle pole body,
which serves as the microtubule attachment necessary for
chromosome segregation during nuclear division. It has
been hypothesized that the spindle pole body is derived
from centrioles through the loss of the 9+2 microtubular
system, though there is no support for this homology
based on detectable sequence similarity. In contrast,
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FIGURE 3 Examples of zygomycete fungal diversity. Zoopagomycota: (a) adult fly
infected by a species of Entomophthorales; (b) Basidiobolus conidium; (c) Conidiobolus
conidia; (d) Zygopolaris thallus with trichospores (photo by R.W. Lichtwardt); (e) Linderina
sporangium; (f) Kickxella sporangium; (g) Rhopalomyces sporangium; (h) Piptocephalis
sporangium. Mucoromycota: (i) Glomus spore (photo from American Society for the Advancement of Science); (j) G. sinuosum sporocarp (photo by D. Redeker); (k) G. mosseae
arbuscule (photo by K. Wex); (l) Mortierella sporangium; (m) Lobosporangium sporangium; (n) Rhizopus sporangium; (o) Thamnidium sporangium; (p) Pilobolus sporangium;
(q) Phycomyces zygosporangium; (r) Cunninghamella zygosporangium; (s) Endogone
sporocarp, zygospore (inset).
Zoopagomycota lineages retain a functional centrosome that possesses a degenerate 9+2 microtubular system (56). Furthermore, there is some evidence that
the genus Olpidium, a zoosporic fungus that retains
its flagellum and infects nematodes and plant roots of
Brassicaceae, may be a member of—or closely related
to—Zoopagomycota (12). Collectively, these observations suggest that Zoopagomycota is critical to understanding the evolution of fungi as they transitioned to
terrestrial ecosystems.
Zoopagomycotina contains a single order, Zoopagales. Species in this order include predators of
nematodes (e.g., Stylopage) and nematode eggs (e.g.,
Rhopalomyces [Fig. 3g]), predators of amoebae (e.g.,
Stylopage, Zoopage), and mycoparasites of mucoralean
fungi (e.g., Syncephalis). Hyphae are small in diameter,
coenocytic, and they form haustoria on or within their
hosts. Asexual reproduction is by conidia or sporangia
according to species, and where known, sexual reproduction is by production of zygospores. Many of these
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fungi are obligate symbionts and thus are difficult to
obtain in axenic culture, and for this reason there is a
paucity of molecular and genomic data. Furthermore,
these fungi are underrepresented in environmental sequence data (57), presumably due to the inadequacy of
existing environmental sampling techniques (e.g., primer
bias, insufficient reference data, etc.), and their internal
transcribed spacer sequences are longer than most fungi,
contributing to underrepresentation (58).
Kickxellomycotina comprises four orders: Asellariales,
Dimargaritales, Harpellales, and Kickxellales. Species
of Kickxellomycotina possess hyphae that are regularly compartmentalized by bifurcate septa that are occluded by a lenticular plug. Asellariales and Harpellales
are associated with digestive tracts of aquatic stages
of arthropods and comprise two of the four orders that
have been treated previously as Trichomycetes (59); the
other two orders, Amoebidiales and Eccrinales, are members of Mesomycetozoea, not the kingdom Fungi (60,
61). Asellariales has filamentous, branched thalli and reproduces asexually by disarticulation of the thalli into
arthrospores. They occur in the digestive tracts of marine,
aquatic, and terrestrial species of isopods and Collembola, where they are thought to function as commensals
(62). Harpellales has branched or unbranched filamentous thalli, and they reproduce by trichospores, which are
asexual spores with hair-like appendages (Fig. 3d). They
attach to the hindgut of aquatic stages of arthropods via
a holdfast and are generally considered to be in a commensal relationship with their host (59). Dimargaritales
species are haustorial parasites of other fungi, with the bestknown species occurring on mucoralean hosts (63), and
Kickxellales includes mycoparasites and saprobes isolated
from soil (64). Dimargaritales and Kickxellales, as well as
Zoopagales, produce unique sporangia called merosporangia. These are cylindrical sporangia that arise from a
bulbous structure, and one or more sporangiospores may
occur in chains within the sporangium (Fig. 3e–h).
Entomophthoromycotina contains three classes, each
with a single order: Basidiobolomycetes and Basidiobolales, Entomophthoromycetes and Entomophthorales,
and Neozygitomycetes and Neozygitales (13, 65, 66).
These fungi are associated with animals as either commensals isolated from animal dung or as pathogens and
parasites of insects. Many species are commonly isolated
from soil and maintained in pure culture, which is consistent with a saprobic life cycle phase. Basidiobolales
is commonly isolated from amphibian dung, although
species are known to occur on the dung of many vertebrates. They produce primary conidia that forcibly
eject a single spore which if it lands on an appropriate
substrate will germinate to form a mycelium or otherwise will undergo repetitive germination, producing a
secondary conidium (Fig. 3b). Under some conditions
nonforcibly discharged capilliconidia are produced from
forcibly discharged conidia. These adhere to the outer
surface of insects (67). Dispersal is then achieved when
the insects are ingested by insectivorous animals, and
after surviving gut passage, the fungus is excreted with
the feces. In a few cases gut infections are known in
various marine and terrestrial vertebrates, and human
gut infections have been mistaken for Crohn’s disease
(68). The ecological function of Basidiobolales is speculative at this time because no definitive functional
experiments have been performed, but its specificity to
animal dung and placement in Zoopagomycota support
an interaction with animal hosts in the digestive system. The phylogenetic placement of Basidiobolales with
molecular- and genome-scale data is problematic. In all
current data sets, it is characterized by long and unstable
branches, and its relationship to other Entomophthoromycotina is unambiguous at this time (69).
Entomophthorales, or literally, insect destroyers, comprises pathogens of insects (Fig. 3a). They infect their
hosts via spores and multiply within the host as oneto two-celled hyphal bodies, which also can function
as gametangia. Upon the host’s death, the fungus ruptures through the cuticle segments, producing forcibly
discharged primary conidia (Fig. 3a). Frequently, infected hosts alight in perched or elevated positions, a
phenomenon known as summit disease, which is thought
to be an induced behavior or adaptation for spore dispersal of the pathogen (20, 70, 71). Neozygitales are
pathogens of insects and mites. They were classified as a
family within Entomophthorales but were distinguished
from Entomophthorales based on the shape and size
of chromosomes (65), although inadequate molecular
data currently exist to test this hypothesis. Neozygites
produces adhesive capilliconidia similar to those of
Basidiobolus (72).
Mucoromycota
Mucoromycota consists of the subphyla Glomeromycotina, Mortierellomycotina, and Mucoromycotina.
Unlike Zoopagomycota, Mucoromycota is characterized by plant associations and plant-based ecologies
(e.g., mycorrhizae, root endophytes, decomposers, etc.).
Some exist as parasites of animals and other fungi,
but these all represent opportunistic infections of hosts
with compromised immune systems or relatively recent derivations from saprobic ecologies (73). Mucoromycota is the sister group to Dikarya, which is also
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characterized by dominant plant-associated life styles,
suggesting that the MRCA of Mucoromycota and
Dikarya corresponds to the origin of modern fungusplant associations, or at least the evolutionary potential
for such relationships.
Glomeromycotina consists of the arbuscular mycorrhizae and Geosiphon, a symbiont of cyanobacteria
(74). Arbuscular mycorrhizae (Fig. 3i–k) are the most
common form of mycorrhizae on the planet, and arbuscule fossils are present among the first land plant fossils
(75–77), confirming an ancient symbiosis. As such, they
are a central taxon in the development of hypotheses
concerning the evolution of early land plants and terrestrial ecosystems (78–80). Despite this importance,
they have been an enigma with respect to phylogenetics of the kingdom Fungi. Morphologically, they resemble zygomycetes in the production of coenocytic
hyphae and terminal or subterminal spores that resemble azygospores (Fig. 3i), asexually formed zygosporelike structures produced terminally on a single hypha
or suspensor cell (81). Sexual reproduction has never
been observed for the group, preventing analysis of
morphological characters traditionally used in classifications. Early molecular phylogenies based on the
small subunit ribosomal DNA resolved the arbuscular
mycorrhizae—with varying statistical support depending on the analysis—as separate from the zygomycetes
and sister to Dikarya (40, 82). However, genome-scale
phylogenies and genome content analyses strongly support the arbuscular mycorrhizae as members of Mucoromycota (13, 83). Recently, mating type genes have
been identified in the Glomeromycotina genomes, and
their structure and diversity are consistent with a functional sexual reproductive cycle without morphological
evidence of sex. Interestingly, the MAT genes are more
similar to those of basidiomycetes than those in other
fungal groups, although this is still a topic of debate (84).
So while we have learned much about Glomeromycotina
from genomic data, where and when these fungi undergo sexual reproduction remains a mystery. Currently,
there are four orders of Glomeromycotina, Archaeosporales, Diversisporales, Glomerales, and Paraglomerales, with Geosiphon being classified in Archaeosporales
(74).
The relationship of Glomeromycotina to the other
subphyla of Mucoromycota is unresolved, with some
analyses resolving it as sister to Mortierellomycotina
and Mucoromycotina, while others resolved it as the
sister group to Mortierellomycotina. The taxon sampling for both Glomeromycotina and Mortierellomycotina is sparse, and expanded taxon sampling is needed
to fully test these rival hypotheses. Mortierellomycotina,
and its sole order Mortierellales, are commonly isolated
soil fungi. They produce zygospores and sporangia similar to some species of Mucorales (Fig. 3l and 3m), the
order in which they were previously classified, but molecular phylogenetics (85) and genome-scale (13) phylogenies both strongly support the taxon as representing
a distinct subphylum. Interestingly, even earlier studies of
sterols separated the two orders because Mortierellales
contain membrane sterols other than ergosterol (86).
These fungi have been demonstrated as root endophytes
of plants (87, 88), but their effect on the host fitness
remains unknown. Some species are reported to have
distinctive odors, perhaps associated with animal dispersal. Mortierellales are also prolific producers of fatty
acids, in particular arachidonic acid, and Mortierella
species are used in its industrial production (89). Both
Glomeromycotina and Mortierellomycotina possess intimate relationships with bacteria, and while facultative, show high levels of specificity and cospeciation (90,
91), and the fungus tends to grow better when cleared
of the bacterium (92). Because of their relationship to
Glomeromycotina, demonstrated plant associations, and
industrial applications including potential alternative
fuels, Mortierellomycotina are the subject of significant
genomic inquiries.
Mucoromycotina contains the remainder of known
zygomycete species and is classified in three orders:
Mucorales, Umbelopsidales, and Endogonales (13).
Mucorales is one of the more commonly isolated groups
of fungi, because many are fast-growing, early colonizers of carbon-rich substrates. Because many species
culture relatively easily, Mucorales are well represented
in culture collections, and their zygospores and sporangia (Fig. 3n–r) are well documented (93). They include taxa that cause economically significant pre- and
postharvest diseases of fruits (e.g., Gilbertella, Mucor,
Rhizopus). They also significantly impact humans both
beneficially through their use in industrial production
of food (e.g., tempeh, Rhizopus) and compounds used
as food supplements (e.g., beta-carotene, Blakeslea),
and antagonistically as rare but increasingly diagnosed
human mycoses (e.g., Mucor, Apophysomyces [94]).
It is among Mucorales that sexual reproduction in fungi
was first demonstrated (95), and numerous species
of Mucorales exhibit phototropic responses to light
(96), making them important eukaryotic model organisms (e.g., Mucor mucedo, Phycomyces blakesleeanus).
Umbelopsidales was recently described for Umbelopsis
(13), a genus of soil-inhabiting fungi that also occurs as
root endophytes (87). Like Mortierella, it was formerly
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classified in Mucorales, but genomic and molecular
analyses support it as a distinct taxon (85). Endogonales
are saprobic or ectomycorrhizal depending on the species (81). Saprobic species occur in heavily decayed
woody substrates, while mycorrhizal species associate
with both nonvascular and vascular plants (78). They
have been argued as important organisms in the colonization of land by green plants (79) and represent an
independent origin of mycorrhizae relative to both Glomeromycotina and Dikarya. It is within Mucoromycota
that the first multicellular sporocarps were produced.
These include independent origins in Endogone (Mucoromycotina [78]) (Fig. 3s) and Modicella (Mortierellomycotina [97]), and as aggregations of spore-producing
hyphae and spores in species of Glomeromycotina
(Fig. 3j) (74). Multicellular sporocarps are not produced
by Zoopagomycota, suggesting that the genetic potential
for complex thallus development did not arise until the
MRCA of Mucoromycota and Dikarya and then resulted in multiple independent inventions of complex
spore-producing structures in Mucoromycota, Ascomycota, and Basidiomycota (98).
DIKARYA
Dikarya is the only described subkingdom of Fungi and
comprises the phyla Ascomycota and Basidiomycota.
The name is based on the nuclear condition of possessing
two genotypically distinct nuclei within the thallus at
some point in the life cycle. The hyphae of Dikarya are
regularly septate, and if a hyphal compartment contains one nucleus or more than one nucleus but all of
the same genotype, it is referred to as monokaryotic or
homokaryotic, respectively. If a hyphal compartment
contains two nuclei of different genotypes, it is referred
to as dikaryotic or heterokaryotic. In Basidiomycota,
basidiospores typically possess one type of nucleus and
germinate to form a monokaryon. Monokaryons fuse
(plasmogamy) with other compatible monokaryons,
producing the dikaryotic state that is maintained by
the products of the mating type genes. The dikaryon
constitutes the major vegetative phase of the life cycle
for most Basidiomycota, and it is as a dikaryon that
most Basidiomycota function in nature (e.g., wood decay, mycorrhizae, pathogens, etc.). Karyogamy occurs
in unique cells, termed basidia, resulting in a shortlived diploid zygote that immediately undergoes meiosis
to produce haploid nuclei that are incorporated into
basidiospores. Importantly, plasmogamy is separated
from karyogamy and meiosis both temporally and spatially. In Ascomycota the dikaryotic state is restricted
to the sexual reproductive cells, with the vegetative
mycelium being homokaryotic. Female gametangia (ascogonia) are fertilized by male gametangia (antheridia)
or gametes (spermatia), resulting in a dikaryotic state
(ascogenous hyphae). A number of rounds of conjugate
nuclear divisions occur prior to karyogamy. Karyogamy and meiosis follow shortly afterward in the young
ascus cell, resulting in homokaryotic ascospores. Thus,
although both phyla of Dikarya have inherited the dikaryotic state from a common ancestor, they are expressed differently in the life cycles of Ascomycota and
Basidiomycota. For more on life cycles of Ascomycota
and Basidiomycota, the reader is directed to general
mycology textbooks (e.g., 41).
More genomes have been sequenced for species of
Ascomycota and Basidiomycota than other phyla of the
kingdom Fungi (http://genome.jgi.doe.gov/fungi/), resulting in an increased resolution of phylogenetic relationships and evolutionary processes that have shaped
phylogenetic and ecological diversity in Dikarya. Ascomycota consists of three subphyla—Taphrinomycotina,
Saccharomycotina, and Pezizomycotina—as does Basidiomycota: Pucciniomycotina, Ustilaginomycotina, and
Agaricomycotina. These subphyla include the majority of
described species of fungi, and most are associated with
plants as symbionts or decomposers of plant materials,
although there are numerous independent transitions
to other hosts and materials (e.g., animals). It is within
Dikarya that we see the apex of multicellular sporocarp
production, complex multicellularity, yet sporocarps
are distributed sporadically across separate subphyla.
Major innovations in sporocarp formation can be found
primarily in Pezizomycotina and Agaricomycotina (98),
but also within a single genus of Taphrinomycotina
(Neolecta [99]) and scattered within Pucciniomycotina
(e.g., Septobasidium [100], Eocronartium, and Jola
[101]). When considering the diversity across the kingdom Fungi, there are a minimum of seven clades of
sporocarp-forming fungi: three in Mucoromycota (discussed above), two in Ascomycota, and two in Basidiomycota. Genomic analyses of evolutionary development,
or EvoDevo, of sporocarp formation are in their infancy,
but a recent study involving Ascomycota paints a complex picture (102). Genes hypothesized to function in
complex multicellularity were present in the MRCA
of Ascomycota and diversified in Pezizomycotina but
were lost in parallel in Saccharomycotina, the budding
yeasts, and the yeast lineages of Taphrinomycotina.
While present, genes that may be necessary for complex
multicellularity did not expand in copy number or show
substantial diversification within Neolecta, thus com-
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plicating a simple explanation of gains and losses of
sporocarps.
Ascomycota (Fig. 4)
Ascomycota is a diverse phylum of fungi that includes
decomposers associated with a myriad of substrates
(e.g., dung, wood, soil), symbionts and associates of
plants and animals, and inhabitants of marine and terrestrial ecosystems. Plant-associated species range from
antagonistic pathogens to beneficial symbionts (e.g.,
mycorrhizae) to foliar, root, and wood endophytes
whose true functions remain unknown. They have impacted our civilization since the dawn of humans with
both positive and negative outcomes. Some ascomycetes
were among the first organisms domesticated by humans
and have been used in fermentation of foods and beverages for over 9,000 years (103). They are the source
of numerous lifesaving drugs including antibiotics,
statins, and immunosuppressants. Unfortunately, they
are also the causal agents of disease, especially of plants,
that have changed continents by removing entire species
from the landscape after introduction by humans (e.g.,
chestnut blight [104]) or have resulted in billions of
dollars of loss in modern agriculture (e.g., Fusarium
head blight [105]). Indeed, our relationship with Ascomycota is one that has profound effects on our planet
and our species.
Taphrinomycotina
The subphylum Taphrinomycotina includes about 140
species with both yeast and filamentous growth forms and
is a sister group to the remaining Ascomycota. Taphrinomycotina is classified into five classes—Taphrinomycetes,
Schizosaccharomycetes, Pneumocystidiomycetes, Neolectomycetes, and Archaeorhizomycetes—each with a
single order. Taphrinomycetes includes plant pathogens
such as Taphrina and Protomyces, which are characterized by saprobic, monokaryotic yeast and pathogenic,
dikaryotic filamentous life stages. Taphrinales has played
an important role in the development of evolutionary
hypotheses of the kingdom Fungi and has been considered a possible evolutionary link between Ascomycota
and Basidiomycota, due to the life cycle described above,
which is similar to that of some smut and other microfungal basidiomycetes of Ustilaginomycotina and Pucciniomycotina. Based on numerous molecular phylogenetic
studies, however, it is strongly supported as a member of
Ascomycota, and it is unclear if the similarity in life cycles
with some Basidiomycota is homologous or not.
Schizosaccharomycetes includes the fission yeasts,
which display an unusual form of cell division for fungi.
Rather than dividing by budding, as is true for all other
yeast forms, cells of Schizosaccharomycetales elongate
and divide into equal cells through the formation of a
fission plate. Schizosaccharomyces pombe is the beststudied species and was originally isolated from millet
beer in East Africa (106). Pneumocystidiomycetes comprises pulmonary pathogens of mammals, including
humans. Species of Pneumocystis are found in soils associated with rodent dens. Pneumocystis jirovecii is an
opportunistic pathogen of humans and is the causal
agent of pneumocystic pneumonia in people with compromised immune systems. Neolectomycetes includes
the only sporocarp-producing species of Taphrinomycotina. The genus Neolecta forms earth tongue-like
sporocarps with a hymenium of asci produced from
uniquely branched hyphae (107). The ecology of the
group is unknown, but the inability to maintain it in
axenic culture suggests a symbiotic association in nature (108). Ancestral character state reconstruction
analyses resolved Neolecta as an independent origin of
sporocarp formation in Ascomycota, unique to that of
Pezizomycotina (98, 109), but comparative genomic
analyses support the possession of common genetic
multicellular machinery between Neolecta and Pezizomycotina (102). Archaeorhizomycetes is the most recently
described class of Taphrinomycotina. It is commonly
detected in environmental sampling of soil and was initially known informally as Soil Clone Group 1 (110, 111).
One species was serendipitously described from a culture
collection of root-associated fungi; it and a second recently
described species are associated with the surfaces of tree
roots (112, 113).
Saccharomycotina
The subphylum Saccharomycotina includes about
1,000 species in a single order, Saccharomycetales,
and 10 major families and several undescribed clades
(114). Saccharomycetales include the majority of the
ascomycete yeasts and are characterized by budding
in asexual reproduction (115). Yeasts, however, have
evolved multiple times in the kingdom Fungi, most likely
through parallel diversification of novel transcription
factors (116). In Saccharomycotina, somatic cells and
hyphae may be haploid or diploid, and diploid cells
undergo meiosis to convert to gametes, which fuse to
form a zygote and develop into asci to produce one to
eight ascospores. Ascogenous hyphae are not produced
as in Pezizomycotina. Two other traits that distinguish Saccharomycetales yeasts from other ascomycetes
occur during ascosporogenesis. These are meiotic divisions with perpendicular spindles developing within the
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FIGURE 4 Examples of Ascomycota diversity. (A) Apothecia (yellow) of Orbilia,
Orbiliomycetes (J. H. Petersen/MycoKey). (B) Apothecia of Aleuria, Pezizomycetes
(J. H. Petertsen/MycoKey). (C) Thallus of Ophioparma with apothecia, Lecanoromycetes (B. McCune, Oregon State University). (D) Thallus of Lichinella, Lichinomycetes
(B. McCune, Oregon State University). (E) Bitunicate asci of Thaxteriella, Dothideomycetes
(S. Huhndorf, Field Museum). (F) Thallus of Arthonia with apothecia, Arthoniomycetes
(B. McCune, Oregon State University). (G) Thallus of Prolixandromyces, Laboulbeniomycetes (A. Weir, SUNY-ESF). (H) Perithecia of Neurospora, Sordariomycetes (N. B. Raju,
Stanford University). (I) Earth-tongue apothecia of Cudonia, Leotiomycetes (Z. Wang, Iowa
State University). (J) Cleistothecia of Eupenicillium, Eurotiomycetes (D. Geiser, Penn State
University). (K) Operculate ascus of Peziza (J. H. Petersen/MycoKey). (L) Ascostroma of
Venturia, Dothideomycetes (T. Volk, University of Wisconsin at La Crosse). (M) Unitunicate
asci Neurospora (N. B. Raju, Stanford University). (N) Prototunicate ascus of Eurotium
(D. Geiser, Penn State University).
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The Fungal Tree of Life
nuclear envelope and formation of ascospores within a
common ascus vesicle instead of ascospores developing
in individual ascus vesicles as in Pezizomycotina (41).
Although they are relatively similar in morphology,
Saccharomycotina yeasts are metabolically diverse. In
common with Taphrinomycotina, Saccharomycotina
lack the septal pore-blocking Woronin bodies characteristic of Pezizomycotina. Earlier yeast taxa were
distinguished by the application of about 100 physiological tests. Previously, hypotheses of relationships
were difficult to address because of the lack of distinctive
morphological characteristics. Now DNA analysis distinguishes yeast species rapidly, as well as providing
phylogenetic hypotheses (114, 115). To expand our
knowledge of biotechnologically important yeasts, a
variety of additional species were sequenced across the
known phylogeny, especially from outside of the betterknown S. cerevisiae clade. This study revealed several
transitions in the early evolution of the ascomycetes,
the synteny of the MAT loci across Ascomycota, and
a genetic code change from CUG-Ser to CUG-Ala in
one lineage (117, 118). Phylogenomic analyses have
also revealed that S. cerevisiae and its relatives are the
product of a whole-genome duplication (119, 120) that
is the result of an ancient hybridization event between
two ancestral species (121).
Yeasts occupy a wide variety of natural (e.g., desert
and forest plants, insect guts, and environments) and
human-provided (e.g., pickle vats, breweries) habitats.
S. cerevisiae is the most widely known yeast in the world
due to its role in bread making and brewing of alcoholic
beverages and as a model organism. This was the first
eukaryotic species to have its entire genome sequenced,
which was justified by its industrial and biological importance. S. cerevisiae and many other yeasts are closely
associated with insects, including bees, dipterans, and
beetles. Certain yeasts display specific associations with
insects and plants, including dipterans and cacti in
American deserts (122), nitidulid beetles and ephemeral
flowers around the world (123), and widely distributed wood-feeding beetles (124). A distinctive group
of previously unknown yeasts related to Suhomyces
tanzawaensis are associated with fungus-feeding beetles
and drosophilids (125). Sexual reproduction and overwintering of S. cerevisiae and its hybrids are promoted
in the gut of social wasps (126). The bodies of human
beings and many mammals are substrates for animal
pathogenic yeasts. Candida albicans and relatives inhabit the digestive tracts of healthy individuals but may
become invasive in those with suppressed immune
systems. Infections can be localized (esophageal candi-
diasis, or thrush; genital candidiasis, or “yeast infection”) or invasive in the brain, heart, bones, and eyes.
Candida can be spread in the blood, a fairly common
infection in hospitals where candidemia has been estimated to be fatal in as many as 19 to 24% of cases (127).
Candida auris, recently recognized as an emerging fungal disease in the United States, is multidrug-resistant
(https://www.cdc.gov/fungal/diseases/candidiasis/candida
-auris.html). Few yeasts are plant pathogens, but Ashbya
gossypii is well known to be destructive to fruit development in cotton (128). This species is also industrially
important because it overproduces riboflavin (129). Interestingly, A. gossypii, and occasionally S. cerevisiae, are
insect-associated.
Pezizomycotina
The subphylum Pezizomycotina contains many more
species than the two other ascomycete subphyla combined; the 63,000 or so species are placed in 13 classes
and 67 orders. Pezizomycotina are mostly filamentous
(130), although many are capable of dimorphic growth.
With the exception of Neolecta (Taphrinomycotina),
they include all of the sporocarp-forming Ascomycota,
but the life cycles of many are only known from their
hyphal and asexual reproductive states. Past classifications of the group have emphasized sporocarp morphology and development and ascus morphology and
dehiscence. Ascomycete sporocarps, or ascomata, were
categorized into four basic types. Apothecia have an
exposed hymenium of asci and are typically cup-shaped
or spathulate (Fig. 4a–d). Perithecia enclose the hymenium in a flask-shaped ascoma, and the ascospores are
released through an opening called an ostiole (Fig. 4h).
Cleistothecia completely enclose an ill-defined hymenium of scattered asci, and no pore or opening is present
(Fig. 4j). (Note: Chasmothecia are another form of
completely enclosed ascomata, but the hymenium exists
as a single basal fascicle of asci.) All three forms of these
ascomata are assumed to be formed after fertilization
of the ascogonium, a form of development called ascohymenial. The fourth major group of ascomata is ascostromata (Fig. 4l). In these fungi, ascogonia are fertilized
in preformed locules, which mature into ascostromata
containing asci and ascospores, a form of development
called ascolocular.
Asci of Pezizomycotina may be operculate or inoperculate. The apex of operculate asci contains a preformed lid, like a manhole cover, that is opened for
ascospore release (Fig. 4k), while inoperculate asci lack
an operculum. Inoperculate asci can be further categorized based on the nature of the ascus walls. Bitunicate
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or fissitunicate asci possess more than one functional
wall layer, an ectoascus and an endoascus (Fig. 4e).
Ascospores are released by the endoascus rupturing
through and extending beyond the ectoascus in a manner reminiscent of a jack-in-the-box. Unitunicate asci
possess a single functional wall layer, and the ascus
apex usually possesses a pore or canal through which
ascospores are released (Fig. 4m). Prototunicate asci
are typically globose and possess a thin ascus wall
that breaks down, or deliquesces, at ascospore maturity
(Fig. 4n). Species that produce prototunicate asci do
not forcibly eject their ascospores. The combinations of
ascomatal and ascal characters can be informative in
describing the overall morphology of a species, but most
traits have been gained and lost multiple times during
the evolution of Pezizomycotina, with a few notable
exceptions (e.g., the operculate ascus of Pezizomycetes).
In addition to the sexual morphs, Pezizomycotina
reproduce prolifically through asexual reproduction in
which the nuclei of spores are products of mitotic divisions. A species can only have one sexual state but may
have many asexual states, a phenomenon called pleomorphy. Many Pezizomycotina are only known from
their asexual morphs, and it is common for a species to
reproduce asexually throughout the growing season but
reproduce sexually only once. Historically, unique Latin
binomials were given to asexual and sexual states, a
system referred to as the dual system of nomenclature,
and thus a single species could have several names. The
reason for this was manifold, but the main argument
was that the sexual and asexual states of Pezizomycotina
could be separated in space and time, so when one observed an asexual state, it could be difficult to link it to a
sexual state. Perhaps the fungus was only observed in its
asexual form by chance; perhaps the sexual form occurs
on a different host or in a different geographic region;
perhaps the fungus only reproduces asexually in axenic
culture; or perhaps the fungus is truly asexual. The advent of molecular data and phylogenetic analyses provided a mechanism to link sexual and asexual morphs
and to identify them as conspecific. For this reason, the
dual system of nomenclature was abolished recently
(131), and all fungi must now be called by only one
name. Needless to say, determining what name to call a
fungus that has many names is no trivial task and is the
subject of much debate, but today students only need to
learn one name for a single species.
Nonlichenized apothecial fungi are classified into
four classes of Pezizomycotina: Orbiliomycetes, Pezizomycetes, Leotiomycetes, and Geoglossomycetes. Orbiliomycetes and Pezizomycetes are sister to the remainder of
the subphylum, but their branching order is unresolved
(132). Orbiliomycetes produce small apothecia with
inoperculate asci. Apothecia typically fruit on wood
or soil, and the asci are small and release ascospores
through an apical slit. The group is best known for its
asexual states of Arthrobotrys, which are predators
of nematodes. These fungi form hyphal rings or loops
that constrict and capture nematodes as they crawl
through the rings. Pezizomycetes produce a diversity of
ascomatal types with operculate asci. Apothecia may be
minute, as in the coprophilous Ascobolus, or large, as
in the type genus Peziza. Some taxa produce apothecia
elevated on a stipe, as in Helvella, or below ground, as in
the prized culinary truffles of Tuber. The asci of all these
taxa are operculate and have a positive amyloid reaction, with the exception of species that form truffles,
which have lost their ability to forcibly discharge their
spores. Leotiomycetes is the largest class of inoperculate
apothecial fungi (133). They produce a myriad of apothecial morphologies ranging from cup fungi to stipitate
earth tongues to hysteriate apothecia that are resupinate and expose the hymenium as a long and slender
slit. At one time all fungi that produce apothecia with
inoperculate asci were classified in Leotiomycetes. Species of the class include important plant pathogens
(Sclerotinia), foliar (Rhytisma) and root (Phialocephala)
endophytes, and mycorrhizae of ericaceous plants (Rhizoscyphus), to name a few. Animal pathogens are also
known, including the recently emerged white nose syndrome of bats (Pseudogymnoascus destructans), which
is devastating brown bat populations of North America
(134). Geoglossomycetes comprise a subset of earth
tongue species (Fig. 4i). These fungi were classified in
Leotiomycetes along with other earth tongue genera
Leotia and Spathularia. Molecular systematic analyses
revealed that Geoglossum and its relatives represent a
separate origin of the earth tongue morphology, however, and a unique class of fungi (135).
Sordariomycetes includes nonlichenized, perithecial
species with inoperculate, unitunicate asci, but species
possessing cleistothecia and/or prototunicate asci are
known to be derived from within perithecial lineages
(133). Perithecia may be produced on well-developed,
stipitate stromata (e.g., as in Xylaria and Cordyceps),
embedded in resupinate (e.g., Hypoxylon) or cushionshaped stromata (e.g., Hypocrea), or superficially in
an aggregated or scattered manner (e.g., Neurospora,
Fig. 4h). Species of the class include some of the most
devastating plant pathogens known. Chestnut blight,
Cryphonectria parasitica, essentially eliminated the
American chestnut from the forests of eastern North
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The Fungal Tree of Life
America and contributed to the development of the
Plant Quarantine Act of 1912. Dutch elm disease,
Ophiostoma ulmi, devastated the American elm and
significantly impacted its presence and abundance on
the landscape and its use as an important urban tree
(136). Fusarium graminearum, head scab of wheat, is a
global pathogen of wheat, one of the most important
grains in human agriculture, and results in losses of
billions of dollars in crop production (105). In addition to plant pathogens, Sordariomycetes are frequently
identified as endophytes through culture and ampliconbased environmental sampling studies (137). Sordariomycetes also includes insect pathogens of Beauveria and
Metarhizium, which are some of the most promising
biological control agents of insect pests in agricultural
ecosystems (138). Some species have recently been
identified as having the potential to grow as an endophyte, suggesting a role in plant protection against insect
pests and a nutritional role of transferring nitrogen to
the plant host (e.g., 72, 139).
Eurotiomycetes are cleistothecial species that produce
prototunicate asci and ascostromatic species that produce bitunicate or fissitunicate asci (140). Cleistothecial
taxa include important industrial and medical species of Aspergillus and Penicillium (Eurotiales) and human pathogens of Coccidioides (Onygenales) that cause
valley fever. These fungi produce both some of the most
potent mycotoxins known to science (aflatoxins of Aspergillus) and lifesaving antibiotics that changed the
course of history (penicillin of Penicillium). There even
exists an independent origin of ectomycorrhizae among
Eurotiomycetes, the genera Elaphomyces and Pseudotulostoma, which form large truffle-like or stipitatecapitate fruiting bodies, respectively (141). Although
Pseudoulostoma and Elaphomyces are members of
Eurotiales, the carbohydrate metabolism of Elaphomyces
granulatus has been shown to be more similar to animal
pathogens in Onygenales than to other members of its
order (142). Ascostromatic species include the black
yeasts (Chaetothyriales) that result in opportunistic cutaneous and subcutaneous infections. Lichenized species
are also represented among the Eurotiomycetes by the
order Verrucariales. These lichens produce perithecioid
ascostromata with bitunicate to fissitunicate asci, representing one of the rare combinations of reported ascohymenial development and bitunicate asci. A third and
unique clade of Eurotiomycetes is Mycocaliciales, which
are saprobes or commensals on lichens (143).
Dothideomycetes is a large and ecologically diverse
class and represents the core of ascostromatic fungi
with bitunicate asci (144). Ascostromata are frequently
perithecioid in appearance and are referred to as pseudothecia (Fig. 4l), but there are apothecioid and cleistothecioid morphologies, as well. The majority of species
are associated with terrestrial plants, and they are commonly identified as endophytes in environmental sampling studies based on cultures and DNA barcodes (e.g.,
137, 145, 146). Numerous taxa diverged from this
ecology, however, including marine fungi of mangroves,
insect pathogens (e.g., Myriangium), mycoparasites
(e.g., Ampelomyces), lichens (e.g., Trypethelium), and
ectomycorrhizae (147). Cenococcum geophilum is one
of the most abundant ectomycorrhizae-formers on the
planet and represents another independent origin of
ectomycorrhizae within the kingdom Fungi (148). Functional genomic studies have demonstrated that C. geophilum plays a role in drought tolerance of host trees,
where it manipulates the host’s response to water stress
(149). The class is best known, however, for its large
number of virulent plant pathogens including Bipolaris
maydis (the causal agent of southern corn blight), Zymoseptoria tritici (Septoria wheat blotch), and Mycosphaerella fijiensis (black sigatoka of banana), to name a few.
Species and races of these fungi frequently produce hostselective toxins that function as pathogenicity factors for
selective host species and genotypes (150, 151).
Because of their importance in agriculture and relative ease of culturing, more than 100 Dothideomycetes
genomes have been sequenced (http://genome.jgi.doe
.gov/programs/fungi/). Published analyses of Dothideomycetes genomes revealed that the structural evolution
of chromosomes is mostly a product of intrachromosomal rearrangements, a phenomenon called mesosynteny (152). Furthermore, disposable chromosomes,
which may be present or absent within an isolate, are
common, but their function is mostly unknown. Comparative analyses of multiple genomes across a phylogenetic and ecological diversity of Dothideomycetes
support the idea that the plant pathogen “play book” is
particularly rich in enzymes for secondary metabolite
production, carbohydrate-active enzymes, small secreted
proteins (SSPs), peptidases, and lipases (153). In addition, genes that encode for effector proteins, which have
a role in pathogenicity, occur often in close proximity
to transposable elements (154), suggesting that transposable elements may play a role in their evolutionary
diversification.
The remaining two classes of nonlichenized Pezizomycotina are Laboulbeniomycetes and Xylonomycetes.
Laboulbeniomycetes is an enigmatic class that is primarily composed of ectoparasites of insects (155–157).
In Laboulbeniales, minute thalli develop from an asco-
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spore through a definitive number of cell divisions and
adhere to the exoskeleton through the production of a
holdfast cell (Fig. 4g). Certain species tend to be host- and
position-specific, with some species being transmitted
through behaviors associated with sexual reproduction
(158). Members of the second order, Pyxidiophorales,
are mostly mycelial mycoparasites with ascospore dispersal by arthropods (159). Xylonomycetes is one of
the more recently described classes of Pezizomycetes and
contains wood endophytes in Xylona (160) and endosymbionts of beetles in Symbiotaphrina, the latter of
which may benefit the insect by detoxifying noxious
plant compounds (161).
The remaining four classes of Pezizomycotina are
Arthoniomycetes, Coniocybomycetes, Lecanoromycetes,
and Lichinomycetes and consist almost entirely of lichenized species (144, 162). Lichens are stable symbioses
between a fungus (mycobiont) and photosynthetic green
alga and/or cyanobacterium (photobiont) that result
in the formation of a thallus unique to the symbiosis.
Lichens are some of the more successful fungal symbioses on the planet and are conspicuous members of
terrestrial ecosystems, where they play important roles
in carbon and nitrogen cycles. The classic definition of a
lichen being formed by one fungus has been challenged
recently, however, by environmental sampling and
microscopy data (163) which demonstrated that basidiomycete yeasts of Cystobasidiomycetes (Pucciniomycotina) were embedded in the cortex. Furthermore, the
presence and abundance of the yeasts correlated with
variations in phenotype. Although there are fewer genomic studies of lichenized than nonlichenized fungi,
current comparative genomic analyses have shed some
light on the formation and maintenance of lichen symbiosis. For example, species of lichenized Pezizomycotina
possess an ammonium transporter/ammonia permease
family that was horizontally transferred from Archaea
but is absent in nonlichenized species (164). Functional
analyses using the lichen-forming fungus Endocarpon
pusillum and its algal partner identified genes involved
in the nitrogen and carbon transfer between symbionts
and lectins required for symbiotic recognition (165).
Lecanoromycetes is the largest and best-studied class
of lichens (162). It includes most of the common forest
lichens and such growth forms as foliose, fruticose,
and crustose lichens. Lichinomycetes and Coniocybomycetes are two smaller classes that form a monophyletic group. Lichinomycetes form gelatinous thalli in
which the cyanobacterial photobiont is not sequestered
in a defined layer of the lichen. Coniocybomycetes form
mazedia, which are stalked ascospore-producing struc-
tures. Mazedial lichens are also known from Caliciales
of Lecanoromycetes, and mazedia are known from
several groups of nonlichenized Pezizomycotina (166).
Arthoniomycetes is the second-largest class of lichens,
and they possess bitunicate asci, although their ascomata
have been interpreted as ascohymenial (144).
Molecular systematics has provided great clarity to
the phylogenetic relationships of the classes of lichenized and nonlichenized Pezizomycotina (109, 167),
but genomic sampling of lichens is still sparse and is
heavily biased toward nonlichenized fungi. Orbiliomycetes and Pezizomycetes are sister to the other classes
of Pezizomycotina, with the remaining classes informally referred to as Leotiomyceta to designate their
monophyly. Within Leotiomyceta, Sordariomycetes,
Laboulbeniomycetes, and Leotiomycetes form a clade,
as do Arthoniomycetes and Dothideomycetes. Eurotiomycetes is sister to Arthoniomycetes+Dothideomycetes,
and the three classes may form a more inclusive clade
with Lecanoromycetes, Coniocybomycetes, Lichinomycetes, and Xylonomycetes, but the relationships are
not unequivocally supported by current data (109, 167).
Finally, Geoglossomycetes appears to represent an isolated lineage of Pezizomycotina (135), but genomic data
are lacking.
Basidiomycota (Fig. 5)
The phylum Basidiomycota is defined by the synapomorphies of basidium and basidiospore. Basidia are
modified terminal hyphal cells that are the site of karyogamy and meiosis. They are typically produced in
hymenial tissues such as gills or pores. Basidiospores
are, with few exceptions, formed on sterigmata, outgrowths of basidia, and typically contain a single haploid nucleus. Basidiospores can either be forcibly ejected
from the sterigma (ballistospores) or passively dispersed (statismospores) by water, wind, or animals.
Most Basidiomycota have a filamentous thallus that is
compartmentalized by regularly distributed septations.
Basidiomycota consists of three subphyla: Pucciniomycotina, Ustilaginomycotina, and Agaricomycotina.
Although reconstruction of the earliest nodes of Basidiomycota has been problematic, genomic studies tend to
support Ustilaginomycotina (smuts and relatives) and
Agaricomycotina (fleshy basidiomycetes) as a monophyletic group that shares an MRCA relative of Pucciniomycotina (e.g., 168). Pucciniomycotina includes yeasts
and filamentous taxa, with the best-known species being
the plant-pathogenic rusts of Pucciniales. Pucciniomycotina and Ustilaginomycotina were formerly classified
in the obsolete class Teliomycetes based on the produc-
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FIGURE 5 Examples of Basidiomycota diversity. Pucciniomycotina: (a) uredinia of
Puccinia iridis; (b) fruiting body of Phleogena faginea; (c) aecia of Coleosporium; (d) yeast
state of Symmetrospora oryzicola. Ustilaginomycotina: (e) smut galls of Ustilago maydis;
(f) gall of Exobasidium; (g) culture of Moniliella sp. Agaricomycotina: (h) culture of
Wallemia; (i) stinkhorn fruiting body of Phallus (photo by Nu Nguyen). (j) coral fruiting
body of Clavaria; (k) crust fruiting body of Amylostereum; (l) club fruiting body of
Clavariadelphis; (m) polypore, conk fruiting body of Pycnoporus; (n) gilled mushroom
fruiting body of Russula; (o) pored mushroom fruiting body of Boletus; (p) puffball fruiting
body of Lycoperdon.
tion of teliospores, which germinate to produce basidia
(as promycelia) and basidiospores, rather than the production of a hymenium.
Former higher-level classifications of Basidiomycota
emphasized the morphology of the basidia and the
nature of basidiospore germination. Phragmobasidia
were described as basidia with some form of septation,
whereas holobasidia lacked septations (169). Heterobasidiomycetes produced basidiospores that could germinate either directly via a germ tube or indirectly via
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secondary spore production or repetitive germination.
Homobasidiomycetes produced basidiospores that germinated directly through germ tube formation only
(170). There is considerable positive correlation between the two systems in that most taxa that produce
phragmobasidia are heterobasidiomycetes, and most
taxa that produce holobasidia are homobasidiomycetes,
but with exceptions. When considered in light of current phylogenetic classifications, heterobasidiomycetes
are found in all three subphyla of Basidiomycota,
and homobasidiomycetes are predominantly found in
Agaricomycotina. Interestingly, the current phylogenetic
classification of subphyla is most consistent with septum morphology (171, 172). Pucciniomycotina possess
a simple septum. Agaricomycotina possess a dolipore
septum characterized by a septum wall that swells near
the septal pore and is bounded by a septal pore cap that
is derived from the endoplasmic reticulum. Ustilaginomycotina possess a range of septum types from simple
pores coupled with membranous pore caps to swollen
pore margins that lack a septal pore cap.
One final important trait in Basidiomycota taxonomy
that we will emphasize here is the clamp connection.
Most basidiomycetes possess a vegetative mycelium that
is dikaryotic, meaning that each hyphal compartment
contains two nuclei. Clamp connections occur in the
dikaryon and function in maintenance of the dikaryotic
nuclear state. Clamp connections are short, modified
hyphal branches that grow away from the hyphal tip
and undergo self-fusion with the main hyphae from
which they branched. Clamp connection formation involves synchronized nuclear divisions and septum formation and results in a clamp-like morphology at the
septum of the main hypha. Clamp connections are found
only in Basidiomycota but are not found in all species
or all tissue types (e.g., monokaryon versus dikaryon,
vegetative hyphae versus sporocarps, etc.).
Molecular phylogenetic and phylogenomic analyses
find greater support for the relationship of Pucciniomycotina as the sister to Ustilaginomycotina and Agaricomycotina than for other arrangements and are consistent
with phragmobasidia and repetitive spore germination
being symplesiomorophic characters inherited from the
MRCA of Basidiomycota. As is also true of Ascomycota,
sporocarp formation may have evolved multiple times
within Basidiomycota, being rare but scattered throughout Pucciniomycotina and common among most lineages of Agaricomycotina (e.g., jelly fungi, mushrooms,
polypores, etc.). The oldest definitive fossil data for
Basidiomycota are septate hyphae with clamp connections from the Pennsylvanian (300 to 360 million years
ago) that occur associated with gymnosperms and ferns
(173, 174). There also exist fossils of mushrooms from
the Cretaceous through the Tertiary (reviewed in reference 16).
Pucciniomycotina
One significant outcome of molecular phylogenetics is
the discovery of the true phylogenetic, morphological,
and ecological diversity of Pucciniomycotina (101,
175). Currently there are 9 classes and over 8,000 species in which yeast and dimorphic growth forms are
common. Basidiocarp formation is rare, but fleshy clavarioid or crust-like forms occur in Pucciniomycetes
(e.g., Eocronartium, Septobasidium), and smaller stilboid and pulvinate basidiocarps are formed in some
Atractiellomycetes (e.g., Phleogena, Hobsonia; Fig. 5b),
Agaricostilbomycetes (e.g., Agaricostilbum), and Microbotryomycetes (e.g., Pycnopulvinus), which presumably
represents an independent origin of sporocarps from
that of Agaricomycotina. Basidia are almost always
phragmobasidia, but unicellular forms (holobasidia) are
known. The unifying character of the subphylum is the
simple septum, which is morphologically similar to the
simple septum of Ascomycota that lacks any septal pore
cap. The majority of species are plant-associated as
pathogens, endophytes, and phylloplane fungi, but there
also exist insect pathogens, orchid mycorrhizae, mycoparasites, and freshwater and marine yeasts. Environmental sequencing studies have revealed unknown
Pucciniomycotina diversity in anoxic deep sea habitats,
Arctic ice, and other extreme environments including
niches characterized by extreme osmotic pressures (reviewed in reference 176). Indeed, the modern concept of
Pucciniomycotina comprises fungi that occupy a diversity of ecological niches comparable to Agaricomycotina
and Pezizomycotina.
The largest class in Pucciniomycotina is Pucciniomycetes, and the best-studied species are plant pathogens in the order Pucciniales, the “rust” fungi, which
collectively attack a wide range of plants from grasses
to trees (Fig. 5a and 5c). These fungi exhibit the most
complex life cycles among the kingdom Fungi, which
include multiple (up to five) spore stages that can occur
on more than one host. For example, Puccinia graminis,
rust of wheat and other grasses, produces monokaryotic spermatia and dikaryotic aeciospores on the alternate host Berberis. Aeciospores infect the primary host,
Triticum, resulting in the production of dikaryotic
urediniospores and teliospores. Karyogamy and meiosis
occur in teliospores, which overwinter in wheat stubble
and germinate in the spring to produce basidia and
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basidiospores, which reinfect the alternate host. Eradication of the alternate host has been applied as one
control method for serious disease caused by rust fungi,
the most famous example being the Barberry Eradication Program for stem rust of wheat that was in effect in
the United States from 1918 to 1980. This program had
a positive impact by reducing the amount of inoculum
available for infecting wheat in the United States during
its implementation (177). This life cycle of occurring on
two hosts is referred to as heteroecious, and the production of all five spore stages is termed macrocyclic.
Not all Pucciniales life cycles are this complex, however; some only occur on one host (autoecious), and
some have lost certain spore stages (demicyclic and
microcyclic). Septobasidiales, also in Pucciniomycetes,
represents one of the more divergent ecologies of Pucciniomycotina in that its members parasitize scale insects
(100, 178). The fungus parasitizes adults of the insect
colony, sterilizing them but not killing them, at least
initially. The insect continues to feed on the host plant,
providing nutrients to the fungus, which in turn provides
shelter to other free-living members of the insect colony.
In addition to Pucciniomycetes, Pucciniomycotina
includes eight other classes that exhibit a range of ecologies and morphologies (175). Members of Agaricostilbomycetes were originally described as ascomycetes
but are now known to be Pucciniomycotina and include
plant saprobes and mycoparasites. Atractiellomycetes
display diverse ecological strategies including mycorrhizae of neotropical orchids. Classiculomycetes include
hyphal species that associate with leaf litter in freshwater
environments but may be capable of mycoparasitism, as
well. Cryptomycocolacomycetes are mycoparasites and
have been isolated from bark beetle galleries. Cystobasidiomycetes are predominantly mycoparasitic yeasts
and include some commonly isolated basidiomycete
red yeasts formerly placed in the anamorphic genera
Rhodotorula and Sporobolomyces (Fig. 5d), as well as
Cyphobasidiales—a yeast lineage recently identified as
comprising a third symbiotic partner in many common
lichen species (163).
Microbotryomycetes, the second-largest class, contains primarily plant pathogens and saprobic phylloplane fungi. The plant pathogens include the “anther
smuts,” Microbotryum violaceum and relatives, which
were originally classified in Ustilaginomycotina because
of the smut-like appearance of the teliospores, a convergent habit of infecting host reproductive tissues.
Most orders of the class contain yeast species that are
common in environmental sampling and represent a
large and poorly characterized diversity (reviewed in
reference 179), including the ubiquitous red yeasts of the
genera Rhodotorula, Sporobolomyces, and Sporidiobolus. Mixiomycetes are an enigmatic monotypic class
that was originally classified in ascomycetes based on
the production of a sac-like spore-producing structure,
although it appears that these spores are mitotic in origin. Mixia osmundae is an intracellular parasite of ferns
but has also been detected in environmental sequencing
of angiosperms, including bamboo and beach (180).
Finally, Tritirachiomycetes are another group that was
originally classified as ascomycete molds. No sexual
state has been observed for the group. It is isolated from
dead plant material and indoor environments and is
suspected of being a mycoparasite of ascomycete molds,
such as Penicillium (181).
Genomic sequencing of Pucciniomycotina is rapidly
advancing and includes some of the largest (Melampsora
allii-populina, 335 Mb; http://genome.jgi.doe.gov/) and
some of the smallest (Mixia, 13.6 Mb [180]) filamentous fungal genomes sequenced to date. Comparison of
pathogenic species of Pucciniomycetes revealed genomic
features related to their biotrophic ecology including
a large number of SSPs, diminished nitrogen and sulfur assimilation pathways, and expanded families of
membrane transporters (182). SSPs along with secreted
hydrolytic enzymes and membrane transporters are
upregulated in planta, consistent with functions in host
infection and nutrient acquisition.
Ustilaginomycotina
The subphylum Ustilaginomycotina includes the smut
fungi and relatives. The majority of species are plant
pathogens, and the term “smut fungi” refers to the black
and powdery masses of teliospores produced on the host
plant. The smut morphology has been derived convergently in Ustilaginomycotina and Pucciniomycotina
(see Microbotryomycetes, Pucciniomycotina) and also
occurs in Entorrhizomycetes. This last class contains a
small cohort of sedge- and rush-associated smut fungi
that cause spore-filled galls to form on host roots. Traditionally placed within Ustilaginomycotina, this group
has recently been elevated to phylum status (183),
although robust phylogenetic and genomic data are
needed to definitively resolve their relationship to other
Dikarya. In Entorrhizomycetes, the septal pore is of the
dolipore type and lacks a septal pore cap, similar to that
of the smut Tilletia (Ustilaginomycotina, Exobasidiomycetes [184]).
The cell walls of Ustilaginomycotina are unique in
that they contain high proportions of glucose and an
absence of xylose, distinguishing them from the rest of
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the Basidiomycota (185). Their hyphal septa can be
swollen near the septal pore, reminiscent of dolipores,
and although they lack a septal pore cap, they may possess a membranous pore cap associated with the septal
pore (reviewed in 186). They also possess a characteristic host-parasite interaction zone defined by fungal
exocytosis of interaction vesicles (179). The genomes of
Ustilaginomycotina are some of the smallest among the
Basidiomycota, ranging from ∼8 Mb and 4,000 genes in
animal-associated yeasts of Malassezia (187) to 24 Mb
and 8,400 genes in phylloplane species of Tilletiopsis
(http://genome.jgi.doe.gov/programs/fungi/).
The subphylum includes important plant-pathogenic
fungi that occur on angiosperms, especially grasses and
sedges, with some exceptions. The majority of Ustilaginomycotina species exhibit a dimorphic life cycle that includes a haploid, saprobic yeast phase and a dikaryotic,
filamentous biotrophic or pathogenic phase. Yeast phases
can be found on numerous plant substrates, and the filamentous phase is initiated by the mating event. Young
basidia become thick-walled and darkly pigmented and
develop into teliospores. Teliospores germinate promycelia
that may be septate (e.g., phragmobasidia of Ustilago) or
not (e.g., holobasidia of Tilletia), depending on the species.
The majority of smut fungi produce basidiospores that are
capable of repetitive germination, giving rise to secondary
spores called sporidia. Sporidia grow and divide as yeasts
until mating between two sporidia reconstitutes the filamentous phase.
Ustilaginomycotina consists of four classes: Exobasidiomycetes, Malasseziomycetes, Moniliellomycetes,
and Ustilaginomycetes. Most species of Exobasidiomycetes produce holobasidia, and teliospores may be
present or absent according to group. Exobasidium
species (Exobasidiales) are biotrophic primarily on
members of Ericaceae (Fig. 5f); they lack a teliospore and
sporulate by producing long holobasidia through stomata or from the epidermis (188). Tilletia (Tilletiales) is
a particularly notorious plant pathogen responsible for
karnal bunt of wheat and diseases of other grasses including barley and rice. It is not known to be dimorphic,
and basidiospores often conjugate on the basidium,
directly giving rise to filamentous dikaryotic growth.
Infections can cause large losses in production, and
contamination of grains with Tilletia teliospores has had
a profound impact on agricultural trade due to plant
quarantine regulations (189).
Malasseziomycetes are lipophilic yeasts. They are
unusual among Ustilaginomycotina in that they are not
plant associated but are found on the skins of mammals including humans. Malassezia species are some-
times referred to as dandruff fungi, and the genomes
of multiple species have been sequenced with the first,
M. globosa, sequenced by Procter & Gamble, the manufacturers of Head & Shoulders shampoo (187). Comparative genomics of multiple species have revealed that
these fungi are incapable of fatty acid biosynthesis and
are dependent upon a lipid-rich diet. To compensate for
its inability to synthesize fatty acids, Malassezia possesses numerous secreted lipases and other hydrolases
for securing host lipids (187, 190). And while Malassezia
species are only known as asexual yeasts, their genomes do possess the genes necessary for mating. Recently, environmental sampling studies have identified
Malassezia as a commonly encountered marine fungus,
although its function in these ecosystems is unknown
(191). Moniliellomycetes also consists of lipophilic
yeasts (Fig. 5g) that were traditionally classified with
other fungi now placed in Agaricomycotina. However,
recent molecular phylogenies suggest it is a distinct classlevel taxon in Ustilaginomycotina (192). Most species
are known from industrial settings, foods, fats, oils,
or substrates with low water activity. The septal pore
apparatus of Moniliella oedocephalis is of the dolipore
type but without pore caps (193), which may further support the current placement within Ustilaginomycotina.
Most Ustilaginomycetes species are dimorphic plant
pathogens and usually produce teliospores in the reproductive organs of their host. Ustilago maydis, corn
smut, is the best-studied species due to corn’s importance
in agriculture as food and biofuel feedstock. The fungus
infects the plant through the developing ovaries but
can colonize all parts of the host, resulting in chlorosis,
anthocyanin formation, and reduced growth. The production of teliospores occurs in kernels of corn that
have been infected by the fungus and coopted for spore
production. The result is that a kernel is transformed
into a large gasteroid “tumor” or gall filled with teliospores (Fig. 5e). Teliospores are darkly pigmented and
produce four-celled phragmobasidia with basidiospores.
Basidiospores divide by budding, producing a haploid
and saprobic yeast phase. Two yeasts of opposite mating
types conjugate to initiate the dikaryotic and pathogenic
filamentous phase of the life cycle. Although the pathogens can be quite destructive on grains, some, such as the
galls of U. maydis, which are a delicacy in Mesoamerica
called huitlacoche, are edible and have gained increasing
popularity in adventure eating in other parts of the
world (194).
Genome analyses of Ustilago revealed a small genome
of approximately 20 Mb encoding less than 7,000 genes
with no known pathogenicity factors (195). Rather,
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SSPs, which exist in small gene families, were demonstrated to function in pathogenicity. These SSPs are
coregulated and expressed in infected tissue, and SSP
mutants exhibited a range of phenotypes from reduced
to increased virulence. The discovery of SSPs and demonstration of their role in infection and pathogenicity
have since transformed the study of biotrophic fungi
including pathogens and beneficial symbionts (196).
Agaricomycotina
Agaricomycotina is currently divided into four classes:
Wallemiomycetes, Tremellomycetes, Dacrymycetes, and
Agaricomycetes. Wallemiomycetes is sister to the remainder of Agaricomycotina and consists of ascomycetelike molds that do not produce sporocarps and are
capable of withstanding conditions of high osmotic
stress (Fig. 5h) (168). Tremellomycetes and Dacrymycetes include the majority of fungi with gelatinous sporocarps, or jelly fungi, while Agaricomycetes includes
some jelly fungi and the remainder of fleshy, sporocarpproducing species (e.g., mushrooms). Tremellomycetes
is sister to Dacrymycetes and Agaricomycetes and contains three orders: Cystofilobasidiales, Filobasidiales,
and Tremellales. Cystofilobasidiales and Filobasidiales
comprise species that are yeasts or are dimorphic, with
sporocarp production being unknown. Tremellales includes many of the well-known jelly fungi (e.g., Tremella
mesenterica, witches butter) and important human
pathogens such as Cryptococcus. Species of Tremella
fruit from wood and produce phragmobasidia with
longitudinal septations dividing the basidium into four
equal compartments with long, slender sterigmata.
Many species in the class are either known or suspected
to be mycoparasites and likely play a role in parasitizing
wood-inhabiting fungi. Cryptococcus is a common inhabitant of soils, plant material (e.g., bark), and bird
guano. It grows primarily as yeast in host tissue but is
dimorphic, producing holobasidia with long chains of
basidiospores. Cryptococcus neoformans is an important human pathogen, especially of people with compromised immune systems, but Cryptococcus gattii is
known to infect immunocompetent people who were
otherwise healthy (197). Dacrymycetes includes a single order, Dacrymycetales, and is the sister group to
Agaricomycetes. Species of this class produce Y-shaped
basidia in gelatinous sporocarps that fruit from wood.
Dacrymycetales are characterized as brown rot fungi in
which wood decay involves the breakdown of cellulose
and hemicellose, but not lignin.
Agaricomycetes comprise the majority of fleshy,
sporocarp-producing basidiomycetes. The diversity of
fruiting bodies includes mushrooms and boletes, polypores and conks, crusts, coral fungi, puffballs and
truffle-like fungi, and stinkhorns. Historically, these
fungi were classified as hymenomycetes and gasteromycetes in a system attributed to Elias Fries in what
is frequently referred to as the Friesian system (198).
Hymenomycetes (hymenial fungi) produce basidia and
basidiospores on a basidia-producing tissue called the
hymenium that is exposed to the environment and forcibly eject their basidiospores. These fungi include the
mushrooms, boletes, corals, crusts, polypores, and conks.
Gasteromycetes (stomach fungi) produce basidia in an
enclosed region of the sporocarp, the gleba, and do not
forcibly eject their basidiospores. Spores may be dispersed by wind and rain, as in the puffballs (Fig. 5p), or
by animal mycophagy or phoresis, as in truffles and
stinkhorns (Fig. 5i), respectively. We now understand
that hymenomycetes and gasteromycetes are artificial
taxa and that these forms are intermixed through the
phylogeny of Agaricomycetes. Molecular phylogenetic
analyses resolve the evolutionary transition in spore dispersal from forcibly discharged to passively discharged
basidiospores, with gasteromycetes being derived from
hymenomycetes on multiple occasions (199, 200). Moreover, most sporocarp morphologies have been derived
multiple times, including the mushroom morphology
characterized by a stipe, a gilled or pored hymenium, and
a cap (Fig. 5n). The evolutionary plasticity of the sporocarp is likely a result of strong evolutionary selection
pressures on production and dispersal of basidiospores.
The modern understanding of Agaricomycetes evolution is the result of numerous studies of molecular phylogenetics (e.g., 201) and evolutionary genomics (e.g.,
17, 202), with the outcome being significant revisions
to the premolecular taxonomy of the class. Currently,
there are 21 orders of Agaricomycetes, with 6 orders
classified in the subclass Agaricomycetidae, 4 in Phallomycetidae, and the remaining 11 treated as incertae
sedis. Auriculariales, Sebacinales, and Cantharellales
represent some of the first orders to diverge since the
MRCA of Agaricomycetes, but the branching order of
these taxa is unresolved. Auriculariales and Sebacinales
include species that produce gelatinous sporocarps and,
in some species, phragmobasidia, providing further evidence that these traits are ancestral for Agaricomycetes.
Cantharellales is best known for prized edible forest
mushrooms of Cantharellus, but the order includes
numerous morphologies including toothed fungi (e.g.,
Hydnum), coral fungi (e.g., Clavulina), and crusts (e.g.,
Botryosphaeria). Phallomycetidae is one of the more
morphologically diverse clades and contains four orders:
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Phallales (the stinkhorns; Fig. 5i), Geastrales (earthstars), Gomphales (coral fungi of Ramaria and cantherelloid fungi of Gomphus; Fig. 5j and 5l), and
Hysterangiales (basidiomycete truffles). Agaricomycetidae contains many of the best-known mushroomforming taxa, including Agaricales and Boletales, but
the modern definition of these orders includes numerous other morphologies. For example, Agaricales also
includes bird’s nests of Nidularia, puffballs of Lycoperdon (Fig. 5p), coral fungi of Clavaria (Fig. 5j), truffles
of Hydnangium, and oyster mushrooms of Pleurotus.
Likewise, in addition to the pored mushrooms of boletes (Fig. 5o), Boletales includes truffles of Rhizopogon,
earthballs of Scleroderma, and resupinate fungi of
Serpula.
Other orders of Agaricomycetidae include crustforming fungi (Atheliales and Jaapiales) and clavarioid
basidiolichens (Lepidostromatales).
The remaining orders of Agaricomycetes mostly include nongilled fungi that were once accommodated in
the concept of Aphyllophorales, an old order name
meaning “without gills” (203). These include the polypores (Fig. 5m), conks, and shelf fungi (Gloeophyllales,
Hymenochaetales, Polyporales, Stereopsidales, Thelephorales, Trechisporales) and the crust or parchment
fungi (Corticiales). Perhaps the most remarkable order
of Agaricomycetes is Russulales. This order of fungi contains all known major morphologies of fleshy sporocarps,
including mushrooms (Russula and Lactarius), polypores (Bondarzewia), tooth fungi (Auriscaplium), crusts
(Aleurodiscus), coral fungi (Clavicorona), and truffles
(Gymnomyces), and it demonstrates the “tricks” that
evolution has played on fungal taxonomists. Interestingly, most of the fungi of Russulales form basidiospores with wall ornamentation that stain blue to black
in iodine solution, the positive amyloid reaction. For a
more complete review of Agaricomycetes systematics and
taxonomy see Hibbett et al. (204).
Agaricomycetes are dominant forest fungi, where they
function as ectomycorrhizal symbionts, tree pathogens,
and agents of wood and litter decay. Comparative and
evolutionary genomics have provided significant insight
into the evolution of these ecologies. Saprobic, or plantdecomposing, Agaricomycetes appear to be the ancestral
ecology, with symbiotic lifestyles such as ectomycorrhizae being more derived. Wood-decay Agaricomycetes
are categorized into two major groups, white rot and
brown rot, although comparative genomic analyses of
wood-decay species reveal the inadequacy of a simple
two-category system (205). White rot fungi are capable
of breaking down cellulose, hemicellulose, and lignin
at roughly equal rates. Brown rot fungi do not break
down lignin to any appreciable degree. The ability to
efficiently break down lignin is attributed to major innovations of wood- and lignin-degrading enzymes, the
fungal class II peroxidases (PODs), in the common ancestor of Agaricomycetes (17). Phylogenomic analyses
support a diversification of PODs in the late Permian,
leading to the hypothesis that the rise of wood-decay
fungi and the diversification of their enzymatic machinery resulted in dramatic decreases in lignified coal deposits at the end of the Permian (17). Brown rot fungi have
been derived multiple times through the loss of fungal
PODs and the ability to degrade lignin. Major white rot
orders include Auriculariales, Hymenochaetales, Corticiales, Polyporales, Russulales, and Agaricales, while
brown rot has evolved independently in Gloeophyllales,
Polyporales, and Boletales.
Ectomycorrhizae (“outer” + “fungus” + “root”) are
fungi that form symbioses with forest trees, especially
species of Pinaceae and Fagaceae. They associate with
the fine roots of the plant, but they do not penetrate
the cells of the plant—thus the term “ecto.” Rather, they
form a sheath around the cortex cells of the fine roots.
The symbiosis is based on an exchange of common
goods, with the fungus providing water and mineral
nutrients (e.g., phosphorus, nitrogen, etc.) to the plant
and the plant providing sugars (e.g., glucose) to the
fungus. Ectomycorrhizae have been derived numerous
times during the evolution of Agaricomycetes, including within Agaricales, Boletales, Russulales, Hymenochaetales, and Cantharellales, and from both white rot
and brown rot ancestors. Comparative genomics have
revealed some consistent themes that allow a fungus
to adopt an ectomycorrhizal lifestyle (197). First, these
fungi lose much of the enzymatic machinery (carbohydrate active enzymes), especially cellulases, associated
with the breakdown of plant cell walls. Second, they have
evolved SSPs that interact with the plant’s host defense
system. Together these attributes allow the fungus to
colonize plant roots and not be identified by the plant
as a hostile intruder. Also, many ectomycorrhizal fungi
exhibit significant genome expansions, but not in gene
content. These genome expansions are due to an increase
in the abundance of transposable elements. The function
of these transposable elements is unknown, but it hypothesized that they may promote genomic adaptations.
SUMMARY
Molecular and genomic analyses of the fungal tree of
life have shown that numerous morphologies empha-
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sized in premolecular classification (e.g., zoospores,
zygospores, fruiting body morphology, etc.) are not
diagnostic of monophyletic groups. Rather, the taxa
that possess these traits experienced more complicated
patterns of diversification and are frequently paraphyletic. The first three lineages to diverge since the LUCA
of kingdom Fungi comprise mostly zoosporic fungi,
Cryptomycota, Blastocladiomycota, and Chytridiomycota. While losses of flagellum are known within the
zoosporic clades and presumably in the MRCA of the
remaining phyla of nonflagellated fungi, the definitive
number and placement of flagellum losses are currently
disputed due to insufficient taxon and data sampling
(e.g., the genus Olpidium). Zygomycete fungi comprise
two separate phyla of nonflagellated fungi: Zoopagomycota and Mucoromycota. They display differences
in host and substrate associations—Zoopagomycota
with animals and fungi, Mucoromycota with plants and
plant substrates—and may represent morphologies and
lifestyles of the first terrestrial fungi. Ascomycota and
Basidiomycota form the Dikarya and possess the most
derived traits, representing the apex of morphological
complexity among the fungi.
Our understanding of fungal evolution has been
significantly influenced by molecular and genome technologies, in both unraveling the aforementioned phylogenetic relationships and illuminating processes of
adaptation and diversification. The sequencing of fungal
genomes is quickly becoming routine, representing the
starting point for an increasing number and types of
studies. This is resulting in a rapid increase in the number of species that can be incorporated into genomescale phylogenies, as evidenced by MycoCosm, with
more than 800 fungal genomes (http://genome.jgi.doe
.gov/fungi/). Continued taxon sampling should exploit
existing resources of biological culture collections to
continue populating the fungal tree of life with genome
data from unsampled species and lineages. Doing
so will not only incorporate the global collecting effort
of mycologists across generations, but it will also add
significant value to existing isolates, making them more
amenable to inclusion in a wider range of research. The
next wave of genome sampling must also incorporate
a greater diversity of fungi that cannot be maintained
in culture. This will require sampling of sporocarps
and spores and will in most cases represent metagenomes with resident populations of bacteria and other
eukaryotes. While this approach is more computationally intensive, extraction of phylogenetically informative markers is tractable (139). Furthermore, significant
progress has been made in grouping sequences by or-
ganism to achieve accurate assemblies of the composite
of individuals within a metagenome (206, 207), and
increased sporocarp sampling will provide more data
examples for refinement of algorithms and computational pipelines. Continued advancements in genomescale phylogenies of fungi are not completely dependent
upon sampling alone, however. Advancements in models
of evolution are needed to understand conflict among
data partitions more accurately and better discern between complicated processes such as incomplete lineage
sorting and insufficient phylogenetic signal (6).
All phylogenetic analyses are inherently biased by
what has been called the “invisible dimension of fungal
diversity” (208). Environmental sampling of ecosystems and niches is consistent with the existence of numerous unknown higher-level lineages (209). While
some of these have been brought into culture and expanded our knowledge of sparsely populated lineages
(e.g., 25, 111), an urgent need to culture more of these
fungi exists, resulting in biological resources necessary
for functional analyses. Currently, the incorporation
of unknown fungi into phylogenetic analyses is limited
to a few loci of limited phylogenetic informativeness
that can be obtained through amplicon-based sampling
approaches. The holy grail of metagenomic sampling
would be the sequencing of, and access to, the complete
genomes of all or most of the organisms in a sample.
Such data would have considerably more explanatory
power within and beyond phylogenetics (e.g., ecological
genomics, EvoDevo, etc.).
Finally, a greater need for integration of other types
of data (e.g., fossils, ecology, physiology, etc.) with genomic data and genome-scale phylogenies exists. Fossils
of fungi are more rarely reported than those of plants
and animals, but the number of researchers studying
paleomycology is as much of a limiting factor as the
fossilization rate of fungi. As more fossils are described,
greater effort should be given to integration of these data
in phylogenies and the development of relaxed clock
methods so that major events in fungal evolution can be
incorporated more accurately into other biological and
geological events of the Earth’s history. Fungal ecology
and ecological genomics are rapidly growing, and significant advancements have been made in understanding evolutionary transitions to mycorrhizal symbioses,
wood decay, and plant pathogenesis. Systematic integration of metagenomic (e.g., short sequence read libraries, metatranscriptomes, etc.) with genome-derived
phylogenies is needed, however, to better understand the
distribution of fungi and fungal metabolic traits across
ecosystems and ecological niches.
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ACKNOWLEDGMENTS
The authors thank Robert W. Lichtwardt, Timothy Y. James, and
Dirk Redecker for the use of images.
This material is based on work supported by the National
Science Foundation (DEB-0090301, DEB-0732993, DEB1441604). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors
and do not necessarily reflect the views of the National Science
Foundation. Francis M. Martin is supported by an ARBRE
Laboratory of Excellence grant (ANR-11-LABX-0002-01) and
the U.S. Department of Energy through the Oak Ridge National
Laboratory Scientific Focus Area for Genomics Foundational
Sciences (Plant Microbe Interfaces Project).
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