Fungal evolution: diversity,taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.     

Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.     

Ancestral Ca2+ signaling machinery in early animal and fungal evolution

Animals and fungi diverged from a common unicellular ancestor of Opisthokonta, yet they exhibit significant differences in their components of Ca2+ signaling pathways. Many Ca2+ signaling molecules appear to be either animal-specific or fungal-specific, which is generally believed to result from lineage-specific adaptations to distinct physiological requirements. Here, by analyzing the genomic data from several close relatives of animals and fungi, we demonstrate that many components of animal and fungal Ca2+ signaling machineries are present in the apusozoan protist Thecamonas trahens, which belongs to the putative unicellular sister group to Opisthokonta. We also identify the conserved portion of Ca2+ signaling molecules in early evolution of animals and fungi following their divergence. Furthermore, our results reveal the lineage-specific expansion of Ca2+ channels and transporters in the unicellular ancestors of animals and in basal fungi. These findings provide novel insights into the evolution and regulation of Ca2+ signaling critical for animal and fungal biology.     

Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor

Lateral gene transfer (LGT) can facilitate the acquisition of new functions in recipient lineages, which may enable them to colonize new environments. Several recent publications have shown that gene transfer between prokaryotes and eukaryotes occurs with appreciable frequency. Here we present a study of interdomain gene transfer of cutinases -- well documented virulence factors in fungi -- between eukaryotic plant pathogens Phytophthora species and prokaryotic bacterial lineages. Two putative cutinase genes were cloned from Phytophthora brassicae and Northern blotting experiments showed that these genes are expressed early during the infection of the host Arabidopsis thaliana and induced during cyst germination of the pathogen. Analysis of the gene organisation of this gene family in Phytophthora ramorum and P. sojae showed three and ten copies in tight succession within a region of 5 and 25 kb, respectively, probably indicating a recent expansion in Phytophthora lineages by gene duplications. Bioinformatic analyses identified orthologues only in three genera of Actinobacteria, and in two distantly related eukaryotic groups: oomycetes and fungi. Together with phylogenetic analyses this limited distribution of the gene in the tree of life strongly support a scenario where cutinase genes originated after the origin of land plants in a microbial lineage living in proximity of plants and subsequently were transferred between distantly related plant-degrading microbes. More precisely, a cutinase gene was likely acquired by an ancestor of P. brassicae, P. sojae, P. infestans and P. ramorum, possibly from an actinobacterial source, suggesting that gene transfer might be an important mechanism in the evolution of their virulence. These findings could indeed provide an interesting model system to study acquisition of virulence factors in these important plant pathogens.     

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative‐genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome‐enabled inferences to envision plausible narratives and scenarios for important transitions.     

DNA分子标记技术在真菌系统学研究中的应用及影响

DNA分子标记技术为真菌系统进化研究提供了许多新的方法,真菌分子系统学已成为一门成熟的学科。简述了真菌分子系统学的发展简史和代表性的研究方法以及对真菌系统学的主要贡献,包括将广义的真菌划分为3个类群,粘菌和卵菌不再属于真菌界成员。真菌生命之树项目的研究结果对真菌界高阶分类系统作出重大调整,将先前的4个门(壶菌门、接合菌门、子囊菌门和担子菌门)变为7个门(微孢子虫门、壶菌门、新丽鞭毛菌门、芽枝霉门、球囊菌门、子囊菌门和担子菌门)和4个亚门,并对真菌各类群概念作出修订。此外,DNA分子标记技术对真菌种概念的认识、有性型-无性型关联及分子生态学等研究领域产生了重要影响。     

Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes

Background  

At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.     

Current knowledge of Chytridiomycota diversity in Northern Europe and future research needs

Chytridiomycota is the most species-rich phylum of basal lineage fungi involved in vital processes in both terrestrial and aquatic ecosystems. Still, the diversity and richness of this group remains cryptic. In Northern Europe, few species have been recorded despite the numerous intact lake systems covering this region. Recent classifications of early diverging fungal lineages differ considerably on the diversity of chytrid species and their taxonomic placement. Here, we present the current knowledge of the Chytridiomycota diversity within Northern Europe by using the Global Biodiversity Information Facility (GBIF) data and compare how this diversity distributes across two recently proposed classification systems. Furthermore, we illustrate how various sampling types are influencing the recorded classification levels. Lastly, we discuss how metabarcoding has contributed to the overall understanding of the Chytridiomycota diversity in revealing the “dark matter fungi”, and we point out future research needs in the field of aquatic mycology in the Nordic region.     

Do miRNAs have a deep evolutionary history?

The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.     

Virulence genes and the evolution of host specificity in plant-pathogenic fungi

In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.     

真核生物系统发育和多样性概观

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.     

Interspecific hybridization in plant-associated fungi and oomycetes: a review

Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.     

Only six kingdoms of life

There are many more phyla of microbes than of macro-organisms, but microbial biodiversity is poorly understood because most microbes are uncultured. Phylogenetic analysis of rDNA sequences cloned after PCR amplification of DNA extracted directly from environmental samples is a powerful way of exploring our degree of ignorance of major groups. As there are only five eukaryotic kingdoms, two claims using such methods for numerous novel 'kingdom-level' lineages among anaerobic eukaryotes would be remarkable, if true. By reanalysing those data with 167 known species (not merely 8-37), I identified relatives for all 8-10 'mysterious' lineages. All probably belong to one of five already recognized phyla (Amoebozoa, Cercozoa, Apusozoa, Myzozoa, Loukozoa) within the basal kingdom Protozoa, mostly in known classes, sometimes even in known orders, families or genera. This strengthens the idea that the ancestral eukaryote was a mitochondrial aerobe. Analogous claims of novel bacterial divisions or kingdoms may reflect the weak resolution and grossly non-clock-like evolution of ribosomal rRNA, not genuine phylum-level biological disparity. Critical interpretation of environmental DNA sequences suggests that our overall picture of microbial biodiversity at phylum or division level is already rather good and comprehensive and that there are no uncharacterized kingdoms of life. However, immense lower-level diversity remains to be mapped, as does the root of the tree of life.     

Pathogenic fungi of marine animals: A taxonomic perspective

Fungi cause diseases in a variety of marine animal hosts. After a thorough review of published literature, we identified 225 fungal species causing infections of 193 animal species, for a total of 357 combinations of pathogenic fungi and marine animal hosts. Among the 193 animal host species, Chordata (100 species, 51.8 %) and Arthropoda (68 species, 35.2 %) were discovered to be the most frequently reported hosts of fungal pathogens. Microsporidia (111 species, 49.3 %) constitutes over half of the described pathogenic fungal species of marine animals, followed by Ascomycota (85 species, 37.8 %), Mucoromycota (22 species, 9.8 %), Basidiomycota (6 species, 2.7 %) and Chytridiomycota (1 species, 0.4 %). Microsporidia primarily parasitize marine arthropods and Teleostei fish, while Basidiomycota are primarily known to cause respiratory diseases of marine mammals. Ascomycota has a diverse host range, from mammals, fish, crustaceans, soft corals and sea turtle. Few Mucoromycota and Chytridiomycota were reported to infect marine animals. Fungal diseases documented in this review likely represent a fraction of fungal diseases in the ocean, where it was estimated to be inhabited by 2.15 million animal species. Intensification of aquaculture practices, global warming and marine pollution may increase fungal disease outbreak of marine animals. All the topics mentioned above will be discussed in greater details in this review.     

Coastal marine habitats harbor novel early-diverging fungal diversity

Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.     

Group I Introns from Zygomycota: Evolutionary Implications for the Fungal IC1 Intron Subgroup

The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subgroup and that they are distantly related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila, which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His–Cys box motif in the antisense strand, a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement of these two introns in basal fungal IC1 intron lineages. This result leads to the suggestion that fungal IC1 introns might have invaded or been transferred laterally after the divergence of the four major fungal phyla. Received: 8 February 2001 / Accepted: 1 November 2001     

Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids

Rare evolutionary events, such as lateral gene transfers and gene fusions, may be useful to pinpoint, and correlate the timing of, key branches across the tree of life. For example, the shared possession of a transferred gene indicates a phylogenetic relationship among organismal lineages by virtue of their shared common ancestral recipient. Here, we present phylogenetic analyses of prolyl-tRNA and alanyl-tRNA synthetase genes that indicate lateral gene transfer events to an ancestor of the diplomonads and parabasalids from lineages more closely related to the newly discovered archaeal hyperthermophile Nanoarchaeum equitans (Nanoarchaeota) than to Crenarchaeota or Euryarchaeota. The support for this scenario is strong from all applied phylogenetic methods for the alanyl-tRNA sequences, whereas the phylogenetic analyses of the prolyl-tRNA sequences show some disagreements between methods, indicating that the donor lineage cannot be identified with a high degree of certainty. However, in both trees, the diplomonads and parabasalids branch together within the Archaea, strongly suggesting that these two groups of unicellular eukaryotes, often regarded as the two earliest independent offshoots of the eukaryotic lineage, share a common ancestor to the exclusion of the eukaryotic root. Unfortunately, the phylogenetic analyses of these two aminoacyl-tRNA synthetase genes are inconclusive regarding the position of the diplomonad/parabasalid group within the eukaryotes. Our results also show that the lineage leading to Nanoarchaeota branched off from Euryarchaeota and Crenarchaeota before the divergence of diplomonads and parabasalids, that this unexplored archaeal diversity, currently only represented by the hyperthermophilic organism Nanoarchaeum equitans, may include members living in close proximity to mesophilic eukaryotes, and that the presence of split genes in the Nanoarchaeum genome is a derived feature.