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Examples of ascomata of Ascomycota. (A) Taphrina deformans. (B) Neolecta vitellina. (C) Peziza sp. (D) Leotia viscose. (E) Microglossum viride. (F) Xanthoria polycarpa. (G) Peltigera membranacea. (H) Opegrapha varia. (I) Dermatocarpon reticulatum. Nonlichenized ascomycetes (A-E), lichens (F-I), hymenoascomycetes (C-G), and loculoascomycetes (H and I). Photographs are courtesy of Joe Ammirati for A, Raymond Boyer for B, Ben Woo for C, Taylor F. Lockwood for D, Mark Steinmetz for E, and Stephen Sharnoff for F-I.
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The mode of evolution of the biologically diverse forms of ascomycetes is not well understood, largely because the descent relationships remain unresolved. By using sequences of the nuclear gene RPB2, we have inferred with considerable resolution the phylogenetic relationships between major groups within the phylum Ascomycota. These relationships a...
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... and 54 ascomycetes. Seven of the 11 classes of Ascomycota were sampled (17). The sources of fungal strains and GenBank accession numbers for RPB2 gene sequences are listed in Table 1, which is published as supporting information on the PNAS web site. The diverse morphologies of some representatives from the major ascomycete lineages are shown in Fig. ...
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... Form of Ascomycetes. Taphrinomycotina are supported as a paraphyletic basal group of ascomycetes by both RPB2 and rDNA data (9,14). This group is highly variable in morphological and biochemical characters, including saprobic and parasitic forms, represented here by Neolecta vitellina (Fig. 2B), the fission yeast Schizosaccharomyces pombe, the human pathogen Pneu- mocystis carinii, and the plant pathogen Taphrina deformans (Figs. 1 A and 2 A). Most members of the group other than Neolecta have a simple body plan, lacking differentiated cells and structures (9). Vegetatively, these organisms grow either uni- cellularly or with ...
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... that the Ascohymenial group is basal and paraphyletic (clades A, B, and C) and that ascolocular fungi are monophyletic and derived (clade D in Fig. 3). The RPB2 phylogeny shows that the apothecial taxa are basal and paraphyletic because apothecia are present in the lineages of the Pezizales, Helotiales, and lichen groups (clades A, B, L, and J in Fig. 3; Fig. 2 C-F). This result was also shown in some phylogenetic analyses based on the 18S rDNA data, but without statistical support (35). Apothecia with interspersed paraphyses and operculate unitunicate asci appear to be the ancestral conditions for Pezizomycotina, as evidenced by the members of Pezizales (Figs. 1C and ...
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... those with prototunicate asci, unitunicate asci with pore dehis- cence, and lecanoralean asci with rostrate dehiscence and bitu- nicate asci with fissitunicate dehiscence. The RPB2 phylogeny shows that the first three of these lichens, all ascohymenial lichens, are a monophyletic group (clade J in Fig. 3). In this clade, lecanoralean lichens (Fig. 2 F and G) with rostrate dehiscence appear to be basal and paraphyletic, suggesting that prototuni- cate and unitunicate asci in lichens are derived from rostrate asci. Ascohymenial lichens (clade J) are closely related to the Sordariomycetes-Helotiales complex (clades H and L), a rela- tionship supported by the shared common features of ascohy- ...
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... taxa Opegrapha (Fig. 2H) and Dermatocarpon (Fig. 2I) were analyzed as representatives of ascolocular lichens with fissitunicate asci. Opegrapha is in the pleosporales complex (clade E) and Dermatocarpon is clustered in Chaetothyriales clade (clade G) in the RPB2 phylogeny (Fig. 3). This result is supported by the presence of paraphysoids in Opegrapha, as is ...
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... taxa Opegrapha (Fig. 2H) and Dermatocarpon (Fig. 2I) were analyzed as representatives of ascolocular lichens with fissitunicate asci. Opegrapha is in the pleosporales complex (clade E) and Dermatocarpon is clustered in Chaetothyriales clade (clade G) in the RPB2 phylogeny (Fig. 3). This result is supported by the presence of paraphysoids in Opegrapha, as is seen for Pleosporales and the ...
Citations
... Briefly, 100 mg of starting material (fruiting body) was used for DNA extraction. The amplification of the nucleotide sequences of the internal transcribed spacer (ITS), 28S large subunit regions of ribosomal DNA (LSU), the translation elongation factor 1-α (TEF1-α), the ribosomal mitochondrial small subunit (mtSSU), and second largest RNA polymerase II regions (RPB2) was conducted via polymerase chain reaction (PCR) using the primer pairs: ITS4/ITS5 [30], LROR/LR5 [31], TEF1-α [32], mtSSU [30], and RPB2-6F/RPB2-7cR [33], respectively. The PCR reaction volume was 25 µL, comprising 12.5 µL of 2× Rapid Taq Master Mix (Vazyme, Nanjing, China), 1 µL of each forward and reverse primer (10 µM) (Sangon, Shanghai, China), and 1 µL of template genomic DNA. ...
The characterization of natural fungal diversity impacts our understanding of ecological and evolutionary processes and can lead to novel bioproduct discovery. Russula and Lactarius, both in the order Russulales, represent two large genera of ectomycorrhizal fungi that include edible as well as toxic varieties. Based on morphological and phylogenetic analyses, including nucleotide sequences of the internal transcribed spacer (ITS), the 28S large subunit of ribosomal RNA (LSU), the second largest subunit of RNA polymerase II (RPB2), the ribosomal mitochondrial small subunit (mtSSU), and the translation elongation factor 1-α (TEF1-α) gene sequences, we here describe and illustrate two new species of Russula and one new species of Lactarius from southern China. These three new species are: R. junzifengensis (R. subsect. Virescentinae), R. zonatus (R. subsect. Crassotunicatae), and L. jianyangensis (L. subsect. Zonarii).
... Both fungi and animals were identified as heterotrophic organisms, but fungi have cell walls (chitinous) [16]. The number of nucleotide substitutions is positively correlated with evolution time, which can estimate the date of evolutionary radiation by determining the number of base changes [17]. Ascomycota, Basidiomycota, and Zygomycota were identified as fungal phyla according to their appearance on the fossilized fungal clamp. ...
... Moreover, protein-coding genes can occur as a single copy with fewer mutations in their exons because of reduced variability in length and reduced ambiguity due to codon constraints. The largest (RPB1) and second largest (RPB2) subunits of the DNA polymerase [17], translation elongation factor 1-alpha (Tef-1α) [51], calmodulin (CaM) [52], and beta-tubulin (Tub2/BenA) [53] genes have been most commonly used for inferring phylogenetic relationships among fungi. Of these, Tub2/BenA is recommended as a partial region of the gene for identifying Penicillium species. ...
A functional identification system is the core and basis of fungal taxonomy, which provides sufficient diagnostic characteristics for species delimitation. Phenotype-based identification systems have exhibited significant drawbacks, such as being laborious and time-consuming. Thus, a molecular-based identification system (rDNA, DNA fingerprint, etc.) is proposed for application to fungi that lack reliable morphological characteristics. High Throughput Sequencing also makes great contributions to fungal taxonomy. However, the formal naming of nonculturable fungi from environmental sequencing is a significant challenge. Biochemical profile-based identification systems have outstanding value in fungal taxonomy and can occasionally be indispensable. This method utilizes biomarker metabolites and proteins that are expected to be unequivocal and stable. Of these, Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry has become the method of choice for chemotaxonomy. In sum, these described identification systems cannot solve all problems of species delimitation, and considerable attention to the updating of fungal nomenclature, standardization of techniques, knowledge sharing, and dissemination will be necessary.
... Due to the low-resolution for ITS rDNA as a speciation and subtyping method, other conserved genes have been evaluated and reportedly deliver better resolution in A. pullulans compared to ITS (Zalar et al., 2008). Coding genes, such as translation elongation factor 1 alpha (TEF1A) (Zalar et al., 2008;Manitchotpisit et al., 2009;Yong et al., 2015), b-tubulin (BT2) (Zalar et al., 2008;Manitchotpisit et al., 2009;Manitchotpisit et al., 2012;Yong et al., 2015;Rodrıǵuez-Andrade et al., 2019), and the RNA polymerase II second largest subunit (RPB2) (Liu and Hall, 2004;Staats et al., 2005;Spatafora et al., 2006;Manitchotpisit et al., 2009;Rodrıǵuez-Andrade et al., 2019) have been used as secondary identification markers for both Aureobasidium and Exophiala cultures. However, our results suggest some challenges to this approach in black yeast result from duplicated genomes. ...
Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including Aureobasidium (n=5) and Exophiala (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as A. pullulans were reassigned as A. melanogenum. Both haploid and diploid A. melanogenum strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.
... On the other hand, the semi-enclosed state appears evolutionarily labile; once evolved, it either transforms into the enclosed state or is lost rapidly (reversal to open), possibly due to the fugacious, incomplete protection it can provide to fruiting body initials. Convergent evolution of closed forms was also speculated in the Pezizomycotina (Ascomycota), where species with open fruiting bodies (apothecia) were basal to those with closed ones (perithecia) (Liu and Hall, 2004). In lichen-forming ascomycetes (Lecanoromycetes) several independent transitions to closed (angiocarp) fruiting bodies were detected (Schmitt et al., 2009). ...
The protection of vulnerable developing structures evolved repeatedly in terrestrial organisms and includes, among others, viviparity in animals and the seed in land plants. In mushroom-forming fungi (Agaricomycetes), sexual spores are born on fruiting bodies, the growth of which is a complex developmental process that is exposed to environmental factors (e.g., desiccation, fungivorous animals). Mushroom-forming fungi evolved a series of innovations in fruiting body protection, however, how these emerged is obscure, leaving the evolutionary principles of fruiting body development poorly known. Here, we show that developmental innovations that lead to the spore-producing surface (hymenophore) being enclosed in a protected environment display asymmetry in their evolution and are associated with increased diversification rates. ‘Enclosed’ development evolved convergently and became a dominant developmental type in several clades of mushrooms. This probably mirrors spore production benefits for species with protected fruiting body initials, by better coping with environmental factors. Our observations highlight new morphological traits associated with mushroom diversification that parallel the evolution of protection strategies in other organisms, such as viviparity or the seed in animals or plants, respectively, but in the context of spore development, highlighting the general importance of protecting vulnerable progeny across the tree of life.
... For example, Basidiomycota fruiting bodies evolved from crust-like forms towards the typical 'toadstool' morphology, i.e., those with cap, stipe and gills ). In the Ascomycota, fruiting bodies evolved from open types, which bear the sporeproducing surface on the upper side open to the environment (called apotheciumtype), towards closed forms in which spore-producing cells (asci) develop internally and shoot spores into the air through various pores/channels (called peritheciumtype; Liu and Hall 2004). ...
... Such attempts by fungal systematists contribute to our understanding of developmental interactions between fungi (McLaughlin et al. 2009) and pave the way for a more reliable categorization of such fungal kingdoms (Hibbett et al. 2007). Among the protein-coding markers (Liu and Hall 2004;Matheny et al. 2002;Reeb et al. 2004;Stiller and Hall 1997), betatubulin (tub2/BenA) (Glass and Donaldson 1995;O'Donnell and Cigelnik 1997) and transforming growth factor 1-alpha (tef1), the highest (RPB1) and second-highest (RPB2) RNA polymerase subunits would be most commonly implemented to establish phylogenetic connections within fungi (James et al. 2006). Moreover, the mini-chromosome management protein (MCM7) shows potential as a newly developed marker, implying higher and lower-level phylogenetic interactions (Gillot et al. 2015;Hustad and Miller 2015;Morgenstern et al. 2012;Raja et al. 2011;Schmitt and Barker 2009). ...
Fungi is a group of eukaryotic and multicellular heterotrophs with a wide range of diversity of phenotypic characters. Therefore, the traditional practice of identifying fungi solely based on morphological characters is incomplete and outdated. With the advancement of molecular biology and bioinformatics, molecular data surge, i.e., DNA and proteins based on which fungal species can be identified. This chapter discusses DNA barcoding techniques using ITS, nuclear ribosomal subunits, protein-coding genes, secondary DNA markers, and DNA taxonomy to identify fungal species and their placement across different taxonomic levels. In addition to the list of curated molecular databases, this chapter provides a step-wise procedure for identifying extremophilic fungi.KeywordsDNA barcodingDNA taxonomyIdentification of extremophilic fungi
... Unicellular species of the phylum have solitary asci (e.g., yeasts). Multicellular species either produce naked asci directly from hyphae, as in some Saccharomycotina and Taphrinomycotina (basal lineages of Ascomycota), or in multicellular structures, ascomata, that vary in shape, the mode of the presentation of the asci, and the development of associated structures (excipula and paraphyses) [6,[8][9][10]. We can differentiate three main types of multicellular ascomata: open (apothecia), closed (chasmothecia, cleistothecia, gymnothecia, stereothecia), and partially closed (perithecia). ...
... Today, we know that closed ascoma have evolved independently in several apothecial lineages. Therefore, this ascomatal type is a homoplastic feature, driven in part by adaptation to environmental factors, and cannot be used at higher levels in phylogenetically-based classifications [9,[11][12][13][14]. ...
Closed cleistothecia-like ascomata have repeatedly evolved in non-related perithecioid and apothecioid lineages of lichenized and non-lichenized Ascomycota. The evolution of a closed, darkly pigmented ascoma that protects asci and ascospores is conceived as either an adaptation to harsh environmental conditions or a specialized dispersal strategy. Species with closed ascomata have mostly lost sterile hymenial elements (paraphyses) and the capacity to actively discharge ascospores. The class Leotiomycetes, one of the most speciose classes of Ascomycota, is mainly apothecioid, paraphysate, and possesses active ascospore discharge. Lineages with closed ascomata, and their morphological variants, have evolved independently in several families, such as Erysiphaceae, Myxotrichaceae, Rutstroemiaceae, etc. Thelebolales is a distinctive order in the Leotiomycetes class. It has two widespread families (Thelebolaceae, Pseudeurotiaceae) with mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, closed ascomata dominate and a great diversity of peridia have evolved as adaptations to different dispersal strategies. The type genus, Thelebolus, is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In this scheme, species with closed ascomata, a lack of paraphyses, and passive ascospore discharge exhibit derived traits that evolved in adaptation to cold ecosystems. Here, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus, involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. We propose a new family, Holwayaceae, within Thelebolales, that retains the phenotypic features exhibited by species of Thelebolus, i.e., pigmented capitate paraphyses and active asci discharge with an opening limitation ring.
... Genomic DNA was extracted by an improved CTAB protocol from dry specimens [22]. In the present study, five loci were amplified and sequenced: 600 base pairs of the ITS region of rDNA using primers ITS1 and ITS4 [23]; 900 base pairs of the 28S nuc rDNA (28S) with primers LR0R and LR5 [24]; 1300 base pairs of the largest subunit of the RNA polymerase II (RPB1) using primers RPB1-AF [25] and RPB1-CR [26]; 700 base pairs of the second largest subunit of the RNA polymerase II (RPB2) with primers bRPB2-6f and fRPB2-7cr [26,27]; and 600 base pairs of the ribosomal mitochondrial small subunit (mtSSU) using primers MS1 and MS2 [23]. The amplified PCR products were subsequently sequenced on an ABI 3730 DNA analyzer using an ABI BigDye 3.1 terminator cycle sequencing kit (Shanghai Sangon Biological Engineering Technology and Services CO., Ltd., Shanghai, China). ...
Three new species are described and illustrated here based on morphological evidence and phylogenetic analysis from China. Russula leucomarginata is recognized by a yellowish red to reddish brown pileus center, a yellowish white to reddish white and sometimes cracked margin, and a reddish white to pastel pink stipe. Russula roseola is characterized by its reddish white to ruby red pileus center, pink to rose margin, adnate to slightly decurrent lamellae with unequal-length lamellulae, reddish white to pink stipe, and occasionally three-celled pileocystidia. Russula subsan-guinaria is morphologically characterized by a reddish brown to dark brown pileus center, a reddish orange to brownish red margin with striation, a reddish white to pink stipe with an expanded base, basidiospores with moderately distant to dense amyloid warts, and hymenial cystidia turning to reddish black in SV. In this study, we performed phylogenetic analysis based on ITS sequence and 28S-RPB1-RPB2-mtSSU datasets. Detailed morphological features and phylogenetic analysis indicate that these three new species belong to Russula subg. Russula.
... This explains the history of life, the relationships among extant species and character states for each species (Vijaykrishna et al. 2006). Most character evolution studies were carried out after the 1990s (Liu and Hall 2004;Li et al. 2005;Schoch et al. 2009;Schmitt 2011;Kumar et al. 2012) and these studies have not been obviously conducted on teleomorphic ascomycetes which lack sequence data. The unavailability of complete sets of sequence data is the major issue for absence of character evolution studies. ...
... This explains the history of life, the relationships among extant species and character states for each species (Vijaykrishna et al. 2006). Most character evolution studies were carried out after the 1990s (Liu and Hall 2004;Li et al. 2005;Schoch et al. 2009;Schmitt 2011;Kumar et al. 2012) and these studies have not been obviously conducted on teleomorphic ascomycetes which lack sequence data. The unavailability of complete sets of sequence data is the major issue for absence of character evolution studies. ...
Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
