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Colony morphologies of C. guamensis (ex-type MCA4658) and C. bombacis (ex-type ATCC 22867). Each fungal isolate was cultured on four different types of media: PDA; CMA; YPGA and YMA. All cultures were incubated at room temperature for 14 days. Bar = 2.5 mm
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Ceraceosorales is a monotypic order in Ustilaginomycotina. Its namesake, Ceraceosorus bombacis, was described as a phytopathogen of Bombax ceiba in India. In this study, we describe Ceraceosorus
guamensis sp. nov., collected on the South Pacific island of Guam, which appears to represent the second isolation of any member of this order in over 40 y...
Citations
... In the smut fungi Ceraceosorus spp. [41], intragenomic variation of ITS sequences varied in up to four sites only, similar to the extent of ITS variability seen in our experiments. Similarly, in a polypore fungus Trichaptum abietinum, three nonorthologous ITS1 types were detected [42] and Type I and Type II ITS1 sequences were found to coexist in all tested T. abietinum strains. ...
Bjerkandera adusta is a species of common white rot polyporoid fungi found worldwide. Despite playing an important role in deadwood decay, the species strains are used in bioremediation due to its ability to degrade polycyclic hydrocarbons and some of them are important etiological agents of chronic coughs and are associated with lung inflammations. In our experiments, diversity within the species was investigated using molecular approaches and we found that sequence diversity seen at ITS sequence level is not due to cryptic speciation but to intragenomic variability of ITS sequences in this species.
... Many examples of enigmatic fungi exist that are only known from the type locality or a few collections in Table 3. Sclerococcum martynii collections studied micromorphologically with ascospore measurements. a restricted geographical area, for example in Ceraceosorales (Ustilaginomycetes), Helotiales (Leotiomycetes), Pyxidiophorales (Laboulbeniomycetes), and Xylariales (Sordariomycetes) (e.g., Haelewaters et al. 2021a;Kijpornyongpan and Aime 2016;Stadler et al. 2020). In the case of S. martynii, more than 20 years of collecting in Guyana Henkel et al. 2012) has only yielded 10 physical collections, but the fungus was also observed, though not collected, in different localities in Guyana within a radius of 200 km. ...
Polydiscidium is an enigmatic, monotypic, and rarely reported genus of Ascomycota of uncertain placement. The morphologically unique Polydiscidium martynii grows on dead wood and forms compound ascomata composed of thick, black, gelatinous somatic tissue that branches out from a common base. Multiple apothecia are located on the branches, mostly toward the tips, and are composed of 8-spored asci and paraphyses embedded in a gelatinous matrix that turns blue in Melzer's reagent. The species was previously known from only three collections from Guyana (holotype), Trinidad, and the Democratic Republic of the Congo and no sequences exist. Due to its peculiar morphology, taxonomic affinities of Polydiscidium have been debated, with different authors having placed it in Helotiaceae, Leotiaceae, or Leotiomycetes incertae sedis. Recent collections of this species resulting from long-term field work in Guyana and Cameroon led us to revisit the morphology and phylogenetic position of this fungus. Newly generated sequences of P. martynii were added to an Ascomycota-wide six-locus data set. The resulting phylogeny showed Polydiscidium to be a member of order Sclerococcales (Eurotiomycetes). Next, a four-locus (18S, ITS, 28S, mtSSU) phylogenetic reconstruction revealed that Polydiscidium is congeneric with Sclerococcum. A new combination is proposed for this species, Sclerococcum martynii. Micromorphological features, including the gelatinous hymenium composed of asci with amyloid gel cap and septate brown ascospores, are in agreement with Sclerococcum. New combinations are proposed for two additional species: Sclerococcum chiangraiensis and S. fusiformis. Finally, Dactylosporales is considered a later synonym of Sclerococcales.
... In the last two decades, several studies reported intragenomic variation in fungi, especially in Basidiomycota, some of them dealt with taxonomic species identifications [55][56][57][58][59]. Most of the studies were conducted through cloning combined with Sanger sequencing or Restriction Fragment Length Polymorphisms (RFLP) profiling [60]. ...
... Some Basidiomycetes fungi including Rhizoctonia solani, Laetiporus sp., and Ogataea ovarum were shown to extensively possess intragenomic variation that confused species identification [57,61,62]. On the other hand, several species of the genera Amanita, Ceraceosorus, Russula, Boletus, Cortinarius, Cantharellus, Lactarius showed very little intragenomic variation, without particular problems for species identification [55,56,58,59,63,64]. Some Ascomycetes, including Phoma exigua, Magnaporthe grisea, Davidiella tassiana, Mycosphaerella punctiformis, Saccharomyces cerevisiae, Teratosphaeria microspora showed a greater amount of intragenomic variation which affected proper species identification [65][66][67]. ...
While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1–D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification.
... Vu et al. (2019) predicted the optimal identity threshold to discriminate filamentous fungal species to be as high as 99.6% for ITS; similar thresholds were determined for basidiomycete yeasts (Urbina and Aime 2018). However, in the phytopathogenic smut genus Ceraceosorus ITS percentage identity within species was found to be <90% (Kijpornyongpan and Aime 2016), and in a recent genomic study of Hypoxylon fragiforme, up to 19 ITS paralogs sharing <97% identity were found within a single genome . Although clearly no single threshold will apply across all fungi, some guidelines for interpreting BLAST results have been detailed in L€ ucking et al. (2020). ...
Using the correct name for phytopathogenic fungi and oomycetes is essential for communicating knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. However, many plant pathogenic fungi are pleomorphic, meaning they produce different asexual (anamorph) and sexual (teleomorph) morphs in their life cycles. Therefore, more than one name has been applied to different morphs of the same species, which has confused users. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi in which a single name for a genus and species can now be used. This move to a single nomenclature, coupled with the advent of molecular systematics and the introduction of polythetic taxonomic approaches, has been the main driving force for a reclassification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging. In this article we outline a series of steps or considerations to greatly simplify this process and provide links to various online databases and resources to aid in determining the correct name. Additionally, a list of accurate names is provided for the most common genera and species of phytopathogenic fungi.
[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
... Both the ITS1 and ITS2 spacer regions are highly variable, and we do not know the extent of this variability in taxa for which no ITS sequence data exist, such as the vast majority of Laboulbeniales genera (Nilsson et al. 2008). An important result of this variability is primer mismatches, such as those identified for Archaeomycetes sequences in the binding site of the commonly used reverse primer ITS4 (Rosling et al. 2011), or for Ceraceosorales sequences in the ITS1 binding site (Kijpornyongpan and Aime 2016), which could have unforeseen consequences in underestimating diversity of fungi based on ITS sequencing only. In time, the design of specific primers (e.g., ITShespL and ITShespR specific for Hesperomyces; Haelewaters et al. 2018a) and next-generation sequencing approaches such as WideSeq allowing for longrange PCR amplification from the SSU to the LSU, thus avoiding that primers need to anneal to the variable ITS spacers (D. ...
This paper describes and illustrates a new species of Laboulbeniales (Ascomycota, Laboulbeniomycetes) recovered from Mastoptera guimaraesi bat flies (Diptera, Streblidae) in Ecuador and Panama. Bat fly-associated Laboulbeniales are still unexplored in the Neotropics, with only four described species of Gloeandromyces and one species of Nycteromyces known. Morphological characteristics and phylogenetic analyses support placement of the new taxon in Gloeandromyces and its recognition as an undescribed species. Gloeandromyces hilleri sp. nov. is easily recognized by 2-3 longitudinal rows of undulations at its perithecial venter. Phylogenetic reconstructions of the large subunit (LSU) ribosomal DNA and the translation elongation factor 1α (TEF1) both resolve G. hilleri and G. nycteribiidarum as sister species. We discuss the utility of LSU and TEF1 as secondary barcodes in Laboulbeniomycetes taxonomy.
... software (Carl Zeiss Microscopy L.L.C, Thornwood, NY). For culture morphology characterization, isolates were grown on Yeast Malt Extract Agar (YMA) and Yeast Peptone Glucose Agar (YPGA) (Kurtzman et al. 2011;Kijpornyongpan and Aime 2016). The colony color was determined using Kornerup and Wanscher (1978), for example: (1A1) represents page 1, column A and row 1. ...
Several interesting Ustilaginaceae yeast morphs were isolated during ongoing surveys of phylloplane-associated fungi in Louisiana (USA) and Guyana. Here we describe Farysia magdalena sp. nov., a phylloplane yeast isolated in southern Louisiana, based on phylogenetic analyses, assimilation profiles and morphological characters, and discuss the yeast morphs in this genus. Additionally, we describe the anamorphic stage of Anthracocystis heteropogonicola, isolated from plant phyllo-planes from the Americas. This is the first report of this fungus in the Western Hemisphere and the first description of the yeast morph for a species of Anthracocystis.
... A growing number of studies is challenging the utility of ITS for delimiting, recognizing and identifying fungal species in certain lineages (O'Donnell and Cigelnik 1997;Nilsson et al. 2008;Bellemain et al. 2010;Pino-Bodas et al. 2013;Kijpornyongpan and Aime 2016;Thiery et al. 2016;Hughes et al. 2018;Kruse et al. 2018a, b;Parks et al. 2019;Tremble et al. 2019;Stadler et al. 2020). A minor problem is that ITS may not amplify in all fungi (Kijpornyongpan and Aime 2016), but sequencing success is better than with many other markers (Schoch et al. 2012). ...
... A growing number of studies is challenging the utility of ITS for delimiting, recognizing and identifying fungal species in certain lineages (O'Donnell and Cigelnik 1997;Nilsson et al. 2008;Bellemain et al. 2010;Pino-Bodas et al. 2013;Kijpornyongpan and Aime 2016;Thiery et al. 2016;Hughes et al. 2018;Kruse et al. 2018a, b;Parks et al. 2019;Tremble et al. 2019;Stadler et al. 2020). A minor problem is that ITS may not amplify in all fungi (Kijpornyongpan and Aime 2016), but sequencing success is better than with many other markers (Schoch et al. 2012). More important caveats include lack of resolution and the potential presence of non-homologous ITS copies in the genome. ...
... Wörheide et al. 2004;Rosselló et al. 2006;Stewart and Cavanaugh 2007). There is also growing evidence in certain fungal lineages (Smith et al. 2007;Simon and Weiß 2008;Lindner and Banik 2011;Kiss 2012;Vydryakova et al. 2012;Wilson et al. 2012;Harrington et al. 2014;Li et al. 2013Li et al. , 2017Kijpornyongpan and Aime 2016;McTaggart and Aime 2018;Colabella et al. 2018;Heeger et al. 2018;Hughes et al. 2018;Stadler et al. 2020). In most fungi, however, the rDNA cistron, including the ITS, appears to follow the principle of concerted evolution (Ganley and Kobayashi 2007). ...
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
... We report new associations and microhabitats of the genus besides Hemileia vastatrix-infected leaves of coffee ; for example, B. tropicalis can also be found in Kweilingia sp.-infected leaves of an unidentified plant, Uromyces sp.-infected leaves of Bidens sp., and finally Puccinia lepturi-infected leaves of Lepturus sp. The description of new species from under sampled geographic regions and microhabitats is essential to enlarging our knowledge of the scope and distribution of fungal diversity (Graff 1917;Case et al. 2012;Kijpornyongpan and Aime 2016), as is the case for the genus Bannoa. ...
The genus Bannoa consists of four described species associated with dead leaves in southwestern Japan. In this study, we describe three new species, Bannoa guamensis, B. rosea, and B. tropicalis, from the South Pacific island of Guam and Guyana in South America. Isolates were obtained from surfaces of diseased and healthy leaves of plants in the Euphorbiaceae, Asteraceae, and Poaceae. DNA sequences from four gene regions, including nuc rDNA internal transcribed spacer ITS1‐5.8S‐ITS2 (ITS), D1–D2 domains of nuc 28S rDNA (28S), nuc 18S rDNA (18S), and a portion of tef1, which encodes translation elongation factor 1-alpha, were produced for phylogenetic analysis. Intercompatibility tests were performed, and subsequent development of clamp connections and basidia were documented for B. tropicalis. Potential life history strategies and association with diseased leaves, including rust-infected leaves, were evaluated across the genus. This is the first report of a species of Bannoa from South America.
... The anamorphic saprobic members of Ustilaginomycotina have previously been classified mainly in the polyphyletic genera Pseudozyma and Tilletiopsis (Begerow et al. 2000;Sampaio 2004;Kurtzman et al. 2011Kurtzman et al. , 2015 and later in several monophyletic genera Acaromyces, Farysizyma, Fereydounia, Jaminaea, Meira, and Sympodiomycopsis (Sugiyama et al. 1991;Boekhout et al. 2003;Inácio et al. 2008;Sipiczki and Kajdacsi 2009;Nasr et al. 2014). Sexual and asexual morphs in Ustilaginomycotina were recently grouped together in order to unify the taxonomy of plant parasites and species known only from their yeast states (Piątek et al. 2015;Wang et al. 2015a; Kijpornyongpan and Aime 2016). As the result, several monophyletic genera (Dirkmeia, Golubevia, Kalmanozyma, and Robbauera) were erected to accommodate species previously classified in the genera Pseudozyma and Tilletiopsis ). ...
The systematic position of three yeast strains isolated from a plant cell culture, a piece of termite nest, or as a foliar endophyte of Coffea arabica, respectively, is evaluated using morphological, physiological, and phylogenetical characteristics. In culture, all three isolates produced white, pale orange to pink colored colonies of cylindrical cells with monopolar budding and pseudohyphae. Standard phenotypic, biochemical, physiological characterization, and phylogenetic analyses of the combined 26S rRNA gene (D1/D2 domains) and ITS region sequences showed the conspecificity of these isolates and suggest their placement within the Exobasidiales (Ustilaginomycotina) as a sister lineage of the sampled and sequenced Graphiola species. Here, we describe this species as Graphiola fimbriata sp. nov. MycoBank MB 825077 (holotype: PC1T; ex-type cultures: IBRC-M 30158T = CBS 13945T = DSM 104832T). This is the first species described in the genus Graphiola for which only the asexual, saprobic developmental phase is known. The description of the genus Graphiola is therefore emended to allow species known only from a saprobic state.
... Most of the South Pacific islands remain under-explored for fungi, although these also appear rich in rare and endemic taxa (e.g. Kijpornyongpan and Aime 2016). Importantly, newly discovered taxa from rare lineages were shown to harbour the majority of novel genes in comparative genomic studies in smut fungi (Kijpornyongpan et al. 2018), highlighting the urgency in documenting this diversity before it disappears. ...
Cintractiella is an unusual genus of smut fungi containing two described species that produce sori as adventitious gall-like spikelets on members of tribe Hypolytreae (subfam. Mapanioideae, Cyperaceae). In September 200, during a botanical expedition on the volcanic island of Kosrae located in the eastern Caroline Islands and within the Federated States of Micronesia, a specimen of Mapania pacifica was collected displaying Cintractiella-like sori in adventitious spikelets on the host leaves. Sori were hypophyl-lous, occurring in groups of spikelets composed of olivaceous-brown scale-like leaves, 1-1.5 mm wide and up to 6 mm long. Microscopic comparison with the protologue and drawings of the type material of C. lamii show several differences in teliospore and sori characters between it and the newly collected material on Mapania. To our knowledge, this represents only the second known collection of any member of Cintractiella on vegetative organs of Hypolytreae and a third species for this genus and the only known smut species infecting Mapania, herein described as Cintractiella kosraensis sp. nov.
