Publications by authors named "M Catherine Aime"

123 Publications

Investigating the Smuts: Common Cues, Signaling Pathways, and the Role of in Dimorphic Switching and Pathogenesis.

J Fungi (Basel) 2020 Dec 16;6(4). Epub 2020 Dec 16.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

The corn smut fungus serves as a model species for studying fungal dimorphism and its role in phytopathogenic development. The pathogen has two growth phases: a saprobic yeast phase and a pathogenic filamentous phase. Dimorphic transition of involves complex processes of signal perception, mating, and cellular reprogramming. Recent advances in improvement of reference genomes, high-throughput sequencing and molecular genetics studies have been expanding research in this field. However, the biology of other non-model species is frequently overlooked. This leads to uncertainty regarding how much of what is known in is applicable to other dimorphic fungi. In this review, we will discuss dimorphic fungi in the aspects of physiology, reproductive biology, genomics, and molecular genetics. We also perform comparative analyses between and other fungi in Ustilaginomycotina, the subphylum to which belongs. We find that lipid/hydrophobicity is a potential common cue for dimorphic transition in plant-associated dimorphic fungi. However, genomic profiles alone are not adequate to explain dimorphism across different fungi.
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http://dx.doi.org/10.3390/jof6040368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766764PMC
December 2020

On the Fly: Tritrophic Associations of Bats, Bat Flies, and Fungi.

J Fungi (Basel) 2020 Dec 12;6(4). Epub 2020 Dec 12.

Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.

Parasitism is one of the most diverse and abundant modes of life, and of great ecological and evolutionary importance. Notwithstanding, large groups of parasites remain relatively understudied. One particularly unique form of parasitism is hyperparasitism, where a parasite is parasitized itself. Bats (Chiroptera) may be parasitized by bat flies (Diptera: Hippoboscoidea), obligate blood-sucking parasites, which in turn may be parasitized by hyperparasitic fungi, Laboulbeniales (Ascomycota: Laboulbeniomycetes). In this study, we present the global tritrophic associations among species within these groups and analyze their host specificity patterns. Bats, bat flies, and Laboulbeniales fungi are shown to form complex networks, and sixteen new associations are revealed. Bat flies are highly host-specific compared to Laboulbeniales. We discuss possible future avenues of study with regard to the dispersal of the fungi, abiotic factors influencing the parasite prevalence, and ecomorphology of the bat fly parasites.
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http://dx.doi.org/10.3390/jof6040361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7770572PMC
December 2020

The integration of Gaussian noise by long-range amygdala inputs in frontal circuit promotes fear learning in mice.

Elife 2020 11 30;9. Epub 2020 Nov 30.

University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, Bordeaux, France.

Survival depends on the ability of animals to select the appropriate behavior in response to threat and safety sensory cues. However, the synaptic and circuit mechanisms by which the brain learns to encode accurate predictors of threat and safety remain largely unexplored. Here, we show that frontal association cortex (FrA) pyramidal neurons of mice integrate auditory cues and basolateral amygdala (BLA) inputs non-linearly in a NMDAR-dependent manner. We found that the response of FrA pyramidal neurons was more pronounced to Gaussian noise than to pure frequency tones, and that the activation of BLA-to-FrA axons was the strongest in between conditioning pairings. Blocking BLA-to-FrA signaling specifically at the time of presentation of Gaussian noise (but not 8 kHz tone) between conditioning trials impaired the formation of auditory fear memories. Taken together, our data reveal a circuit mechanism that facilitates the formation of fear traces in the FrA, thus providing a new framework for probing discriminative learning and related disorders.
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http://dx.doi.org/10.7554/eLife.62594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7704104PMC
November 2020

Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi.

PeerJ 2020 4;8:e10110. Epub 2020 Nov 4.

Agricultural Research Service, Southeastern Fruit and Tree Nut Research Laboratory, United States Department of Agriculture, Byron, GA, United States of America.

is an invasive alien ladybird in North America and Europe. Studies show that multiple natural enemies are using as a new host. However, thus far, no research has been undertaken to study the effects of simultaneous infection by multiple natural enemies on . We hypothesized that high thallus densities of the ectoparasitic fungus on a ladybird weaken the host's defenses, thereby making it more susceptible to infection by other natural enemies. We examined mortality of the North American-native and co-infected with and an entomopathogenic fungus-either or . Laboratory assays revealed that -infected individuals are more susceptible to entomopathogenic fungi, but does not suffer the same effects. This is in line with the enemy release hypothesis, which predicts that invasive alien species in new geographic areas experience reduced regulatory effects from natural enemies compared to native species. Considering our results, we can ask how affects survival when confronted by other pathogens that previously had little impact on .
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http://dx.doi.org/10.7717/peerj.10110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648450PMC
November 2020

in the Guineo-Congolian rainforest: Epitypes and new species from the Dja Biosphere Reserve, Cameroon.

Mycologia 2021 Jan-Feb;113(1):168-190. Epub 2020 Nov 11.

Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907.

Four epitypes and three new species of (Amanitaceae, Agaricales, Agaricomycetes, Basidiomycota) are described from Guineo-Congolian rainforests of Cameroon. , and are epitypified based on collections that are the first since the species were described nearly a century ago. Morphological features of the epitypes are described and enumerated. , and are described as new and added to the known macromycota of tropical Africa. Habit, habitat, and known distribution are provided for each species. Sequence data for the internal transcribed spacer (ITS) locus are provided for types and other collections of all taxa, and a molecular phylogenetic analysis across the genus corroborates morphology-based infrageneric placement for each.
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http://dx.doi.org/10.1080/00275514.2020.1816386DOI Listing
November 2020

Marasmioid rhizomorphs in bird nests: Species diversity, functional specificity, and new species from the tropics.

Mycologia 2020 Nov-Dec;112(6):1086-1103. Epub 2020 Sep 8.

Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907.

In tropical and subtropical rainforests, vegetative fungal rhizomorphs from the Marasmiineae are routinely used as construction material in bird nests. Because rhizomorphs seldom produce mushrooms within nests, the fungal species involved remain largely unknown. In turn, this limitation has prevented us from resolving broader questions such as whether specific fungal species are selected by birds for different functional roles (i.e., attachment, or parasite control). To fill some of these gaps, we collected 74 rhizomorph-containing bird nests from the Neo- and Afrotropics and used nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) sequences to discriminate between rhizomorph-forming species. In total we recovered 25 Marasmiineae species used by birds in nest construction, none of which were shared between the Neotropics and the Afrotropics. We also collected Marasmiineae basidiomes in the vicinity of nests and used ITS sequences to match these sporulating morphs with nest rhizomorphs for nine species. Basidiomes from an additional five species were found fruiting from rhizomorphs incorporated within bird nests. Finally, an additional six species were putatively identified based on publicly available sequence data. Rhizomorphs of five species were found to be utilized almost exclusively as lining material in nests. Lining material comes in direct contact with nestlings and is hypothesized to play a role in parasite control. Rhizomorphs from 10 species were used to attach and anchor nests to substrates; we matched six of those to fruiting litter trap-forming species collected in the understory. Litter traps hold large quantities of fallen litter material, suggesting that birds may preferentially use rhizomorphs that are adapted to bearing heavy loads for nest attachment. Finally, we describe two species of , sp. nov., and , sp. nov.-that are commonly found associated with bird nests and show that rhizomorph production is common across the genus.
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http://dx.doi.org/10.1080/00275514.2020.1788892DOI Listing
September 2020

Identification and Characterization of Fungi Causing Thread Blight Diseases on Cacao in Ghana.

Plant Dis 2020 Nov 21;104(11):3033-3042. Epub 2020 Aug 21.

Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705, U.S.A.

(chocolate tree) is currently under serious threat from thread blight disease (TBD), which has been attributed to the causal agent in other regions of the world. TBD in Ghana has similar symptomology but variable signs. This study sought to determine whether TBD in Ghana was caused by a single agent and whether was a significant agent of TBD. Forty-eight isolates were collected from eight geographical locations in Ghana for morphological and molecular characterization. Disease signs occurred as vegetative rhizomorphs or hyphal aggregates, which were classified into five morphotypes: A, abundant thin, black, "horse hair"-type rhizomorphs; B, scattered brown rhizomorphs; C, whitish to brownish-white; D, faint cream or dull white; and E, aggregates of shiny or silky white hyphae. Sequencing and analyses of three loci-the internal transcribed spacer region of the nuclear ribosomal repeat, nuclear large subunit, and mitochondrial small subunit-detected four species, all members of the Marasmiaceae, causing TBD-like disease. These were identified as (morphotype A), (morphotypes B and C), (morphotype E), and (morphotype D). , the most frequently isolated TBD fungus in this study, is primarily an Asian fungus and not previously associated with diseases of cacao. , the second most frequently isolated fungus, is a pan-tropical pathogen with a broad host range; this is the first report of the fungus causing TBD on cacao. also has a broad pan-tropical distribution and host range and causes thread blight on several tropical tree crops. Surprisingly, , the most frequently cited agent of TBD in cacao, made up only 8% of the isolates.
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http://dx.doi.org/10.1094/PDIS-03-20-0565-REDOI Listing
November 2020

The History of Cacao and Its Diseases in the Americas.

Phytopathology 2020 Oct 14;110(10):1604-1619. Epub 2020 Sep 14.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A.

Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, , originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the "blast". Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches' broom disease in the late 1980s. Today, most of the world's cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.
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http://dx.doi.org/10.1094/PHYTO-05-20-0178-RVWDOI Listing
October 2020

A new species of from Ecuador and Panama revealed by morphology and phylogenetic reconstruction, with a discussion of secondary barcodes in Laboulbeniomycetes taxonomy.

Mycologia 2020 Nov-Dec;112(6):1192-1202. Epub 2020 Jul 27.

Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907.

This paper describes and illustrates a new species of Laboulbeniales (Ascomycota, Laboulbeniomycetes) recovered from bat flies (Diptera, Streblidae) in Ecuador and Panama. Bat fly-associated Laboulbeniales are still unexplored in the Neotropics, with only four described species of and one species of known. Morphological characteristics and phylogenetic analyses support placement of the new taxon in and its recognition as an undescribed species. 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 () both resolve and as sister species. We discuss the utility of LSU and as secondary barcodes in Laboulbeniomycetes taxonomy.
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http://dx.doi.org/10.1080/00275514.2020.1781496DOI Listing
July 2020

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus 2020 10;11:14. Epub 2020 Jul 10.

International Commission on the Taxonomy of Fungi, Champaign, IL USA.

True fungi () and fungus-like organisms (e.g. , ) 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.
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http://dx.doi.org/10.1186/s43008-020-00033-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353689PMC
July 2020

Red yeasts from leaf surfaces and other habitats: three new species and a new combination of ().

Fungal Syst Evol 2020 Jun 20;5:187-196. Epub 2019 Dec 20.

Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.

Our understanding of the systematics of red yeasts has greatly improved with the availability of sequence data and it is now clear that the majority of these fungi belong to three different classes of (): , , and . Despite improvements in phylogenetic placement, the taxonomy of these fungi has long been in need of revision and still has not been entirely resolved, partly due to missing taxa. In the present study, we present data of culture-based environmental yeast isolation, revealing several undescribed species of , which was recently introduced to accommodate six species previously placed in the asexual genera and in the / clade of . Based on molecular phylogenetic analyses of three rDNA loci, morphology, and biochemical studies, we formally describe the following new species: . from leaf surfaces in Portugal and the USA; . from leaf surfaces in Brazil, and the USA and decaying wood in the USA; and . from a beetle gut in the USA, leaf surfaces in Brazil and marine water in the Taiwan and Thailand. Finally, we propose a new combination for based on our molecular phylogenetic data, .
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http://dx.doi.org/10.3114/fuse.2020.05.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7250012PMC
June 2020

New species of .

Fungal Syst Evol 2020 Jun 26;5:151-167. Epub 2019 Nov 26.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

Six species of (, , ) are described from recent Cameroonian collections: , , , , , and .These species occur in tropical rainforests dominated by ectomycorrhizal trees in the genera and Data on macromorphology, micromorphology, DNA sequences, habitat and comparisons with similar taxa are provided for each. This is the first contemporary taxonomic work on the from Cameroon.
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http://dx.doi.org/10.3114/fuse.2020.05.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7250018PMC
June 2020

New species of subgen. from Guyana.

Fungal Syst Evol 2019 Jun 28;3:1-12. Epub 2018 Nov 28.

Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA.

New species of subgen. are described from Guyana. sp. nov. sp. nov. and sp. nov. represent the latest additions to the growing body of newly described ectomycorrhizal fungi native to -dominated tropical rainforests. Macro- and micromorphological characters, habitat, and DNA sequence data for the ITS, nrLSU, , and are provided for each taxon, and β- for most. Distinctive morphological features warrant the recognition of the three new species and a molecular phylogenetic analysis of taxa across subgen. corroborates their infrageneric placements.
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http://dx.doi.org/10.3114/fuse.2019.03.01DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235980PMC
June 2019

, sp. nov., a newly described rust on the federally endangered plant, California sea-blite ().

Mycologia 2020 May-Jun;112(3):543-551. Epub 2020 May 6.

Foreign Disease-Weed Science Research Unit, Agricultural Research Service , United States Department of Agriculture, Fort Detrick, Maryland 21714.

Rust disease was observed on populations of near Morro Bay, California. The pathogen was identified as a species of based on teliospore and urediniospore morphology and nuc 28S rDNA sequence analysis. The isolate was compared with previously described species of that infect members of Chenopodiaceae, prompting a taxonomic reevaluation of species on . Herein, is described. It can be differentiated from the closely related (syn.: ) based on host range, teliospore morphology, and 28S sequence data. The new combination, , is made for , the oldest name for Eurasian rust. Finally, it was determined that likely does not occur in the United States and that the rust of in the United States likely comprises a third, yet unnamed taxon, different from both and . This is the first record of a rust fungus on . An identification key for species reported on Chenopodiaceae is provided.
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http://dx.doi.org/10.1080/00275514.2020.1739602DOI Listing
May 2020

Studies of Neotropical tree pathogens in : a new species, , and new combinations for and .

MycoKeys 2020 30;66:39-54. Epub 2020 Mar 30.

Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, 47907-2054, USA Purdue University West Lafayette United States of America.

The crinipelloid genera and (Agaricales, Marasmiaceae) are characterized by basidiomes that produce long, dextrinoid, hair-like elements on the pileus surface. Historically, most species are believed to be saprotrophic or, rarely, parasitic on plant hosts. The primary morphological diagnostic characters that separate and are pliant vs. stiff () stipes and a tendency toward production of reddish pigments (ranging from violet to orange) in the basidiome in . Additionally, most species of appear to have a biotrophic habit, while those of are predominantly saprotrophic. Recently, several new neotropical collections prompted a morphological and phylogenetic analysis of this group. Herein, we propose a new species and two new combinations: , described from Belize, is characterized by its larger pileus and narrower basidiospores relative to other related species; (= ) is recollected and redescribed from biotrophic collections from northern Argentina; and (= ), a parasite of . The addition of these three parasitic species into support a hypothesis of a primarily biotrophic/parasitic habit within this genus.
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http://dx.doi.org/10.3897/mycokeys.66.48711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136302PMC
March 2020

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species.

Stud Mycol 2020 Jun 28;96:17-140. Epub 2020 Jan 28.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the (). The other 61 are distributed in 26 genera in the . Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.
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http://dx.doi.org/10.1016/j.simyco.2020.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082220PMC
June 2020

, sp. nov., a member of the species complex recovered from pseudoflowers on yellow-eyed grass ( spp.) from Guyana.

Mycologia 2020 Jan-Feb;112(1):39-51. Epub 2019 Dec 11.

Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-2012.

We report on the discovery and characterization of a novel species that produced yellow-orange pseudoflowers on spp. (yellow-eyed grass; Xyridaceae) growing in the savannas of the Pakaraima Mountains of western Guyana. The petaloid fungal structures produced on infected plants mimic host flowers in gross morphology. Molecular phylogenetic analyses of full-length (RNA polymerase largest subunit), (RNA polymerase second largest subunit), and (elongation factor 1-α) DNA sequences mined from genome sequences resolved the fungus, described herein as , sp. nov., as sister to within the African clade of the species complex. Results of a polymerase chain reaction (PCR) assay for mating type idiomorph revealed that single-conidial isolates of had only one of the idiomorphs ( or ), which suggests that the fungus may have a heterothallic sexual reproductive mode. BLASTn searches of whole-genome sequence of three strains of indicated that it has the genetic potential to produce secondary metabolites, including phytohormones, pigments, and mycotoxins. However, a polyketide-derived pigment, 8--methylbostrycoidin, was the only metabolite detected in cracked maize kernel cultures. When grown on carnation leaf agar, is phenotypically distinct from other described species in that it produces aseptate microconidia on erect indeterminate synnemata that are up to 2 mm tall and it does not produce multiseptate macroconidia.
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http://dx.doi.org/10.1080/00275514.2019.1668991DOI Listing
September 2020

New species of described from the tropics and the first report of the genus in South America.

Mycologia 2019 Nov-Dec;111(6):953-964. Epub 2019 Oct 21.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907.

The genus consists of four described species associated with dead leaves in southwestern Japan. In this study, we describe three new species, , and , 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 , 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 . 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 from South America.
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http://dx.doi.org/10.1080/00275514.2019.1647397DOI Listing
June 2020

Variation in the Internal Transcribed Spacer Region of and Implications for Molecular Diagnostic Assays.

Plant Dis 2019 Sep 12;103(9):2237-2245. Epub 2019 Jul 12.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A.

, the causal agent of soybean rust (SBR), is a global threat to soybean production. Since the discovery of SBR in the continental United States, quantitative polymerase chain reaction assays based on the internal transcribed spacer (ITS) ribosomal DNA locus were established for its rapid detection. However, insufficient data were initially available to test assays against factors that could give rise to misidentification. This study aimed to reevaluate current assays for (i) the potential for false-positive detection caused by nontarget species and (ii) the potential for false-negative detection caused by intraspecific variation within the ITS locus of A large amount of intraspecific and intragenomic variation in ITS was detected, including the presence of polymorphic ITS copies within single leaf samples and within single rust sori. The diagnostic assays were not affected by polymorphisms in the ITS region; however, current assays are at risk of false positives when screened against other species of . This study raises caveats to the use of multicopy genes (e.g., ITS) in single-gene detection assays and discusses the pitfalls of inferences concerning the aerobiological pathways of disease spread made in the absence of an evaluation of intragenomic ITS heterogeneity.
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http://dx.doi.org/10.1094/PDIS-08-18-1426-REDOI Listing
September 2019

Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.

Syst Biol 2020 01;69(1):17-37

Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary.

Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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http://dx.doi.org/10.1093/sysbio/syz029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115942PMC
January 2020

Genetic Diversity of Stenocarpella maydis in the Major Corn Production Areas of the United States.

Plant Dis 2017 Dec 11;101(12):2020-2026. Epub 2017 Oct 11.

Department of Botany and Plant Pathology, Purdue University.

The fungus Stenocarpella maydis (Berk.) B. Sutton, causal agent of Diplodia ear rot, is a prevalent corn (Zea mays L.) pathogen in the United States. Although S. maydis reduces grain quality, causes yield loss, and can produce mycotoxins in some countries, few studies have examined its biology and genetic diversity. We analyzed the genetic diversity of 174 S. maydis isolates sampled across the major corn production areas in the United States using nine different microsatellites. In all, 55 unique multilocus genotypes (MLG) were observed out of the 174 S. maydis isolates tested. After conducting a Bayesian clustering analysis by STRUCTURE, it was observed that the most probable number of genetic groups was two; however, no separation by their geographical location was identified. According to the minimum spanning network, the S. maydis population is linked across geographic regions of the United States but also contains private genotypes. Temporal diversity in the inoculum source was also observed at one location across 4 years. The haploid stage of S. maydis was confirmed and both mating type genes were amplified among selected isolates with unique MLG. We theorize that, although S. maydis is primarily an asexual fungus, sporadic cryptic recombination may occur, which could contribute to the genetic diversity observed in this study.
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http://dx.doi.org/10.1094/PDIS-02-17-0292-REDOI Listing
December 2017

The Suhomyces clade: from single isolate to multiple species to disintegrating sex loci.

FEMS Yeast Res 2019 03;19(2)

Department of Biological Sciences, Louisiana State University; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.

Candida tanzawaensis clade members are now placed in Suhomyces. The group was virtually unknown until the early 2000s. Here, we review progress made on Suhomyces over the last two decades and provide data from reports of new members of the group from distant localities worldwide, their habitats and a new study of mating loci that helps explain earlier failed compatibility tests. Phylogenetic studies indicate early diverging members are mostly associated with plants, but later diverging species are usually fungus-feeding insect associates. The genome of S. tanzawaensis was known to have a heterothallic mating allele arrangement with a single MAT α idiomorph. For this review, we generate sequence data and compare the MAT gene arrangement of 30 strains from nine Suhomyces species. These varied from MAT α loci containing mating genes α1 and α2, hypothetical MAT a loci without detectable mating genes a1 and a2 to truncated, possibly completely dissociated MAT loci with intraspecific variation. The absence of a second MAT in a genome locus precludes the possibility of mating type switching. Sympatric speciation likely occurred after MAT locus deterioration began in isolated habitats. Although asexual reproduction may be an effective short-term strategy, theory predicts it will not endure over the extreme long term.
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http://dx.doi.org/10.1093/femsyr/foy125DOI Listing
March 2019

A new species of (Ustilaginales) from the volcanic island of Kosrae, Caroline Islands, Micronesia.

MycoKeys 2018 6(42):1-6. Epub 2018 Nov 6.

National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, HI 96741, USA Department of Botany, Iranian Research institute of Plant Protection Tehran Iran.

is an unusual genus of smut fungi containing two described species that produce sori as adventitious gall-like spikelets on members of tribe (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 was collected displaying -like sori in adventitious spikelets on the host leaves. Sori were hypophyllous, 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 show several differences in teliospore and sori characters between it and the newly collected material on . To our knowledge, this represents only the second known collection of any member of on vegetative organs of and a third species for this genus and the only known smut species infecting , herein described as
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http://dx.doi.org/10.3897/mycokeys.42.27231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234224PMC
November 2018

in North America: distribution and natural host range.

MycoKeys 2018 11(39):63-73. Epub 2018 Sep 11.

Purdue University, Department of Botany and Plant Pathology, West Lafayette, Indiana, USA Purdue University West Lafayette United States of America.

, a rust fungus pathogen of Carolina bristlemallow, (Malvaceae), is newly reported from North America, appears to be well established along the Gulf coast and is likely to have been introduced from South America. Its taxonomy, distribution and natural host range are discussed and a lectotype designated for this species. and are reported as new hosts for the rust. Additional new records for Malvaceae rusts are made for on from Brazil, on in Florida and on sp. in Peru. Finally, an identification key for the microcyclic species on members of Malvaceae in North America is provided.
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http://dx.doi.org/10.3897/mycokeys.39.27378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160790PMC
September 2018

An analysis of codon bias in six red yeast species.

Yeast 2019 01 16;36(1):53-64. Epub 2018 Oct 16.

Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy.

Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.
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http://dx.doi.org/10.1002/yea.3359DOI Listing
January 2019

The power of discussion: Support for women at the fungal Gordon Research Conference.

Fungal Genet Biol 2018 12 24;121:65-67. Epub 2018 Sep 24.

Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA.

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http://dx.doi.org/10.1016/j.fgb.2018.09.007DOI Listing
December 2018

New Records of Rust Disease Caused by Uromyces halstedii in North America.

Plant Dis 2018 Sep 4:PDIS02180261PDN. Epub 2018 Sep 4.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907.

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http://dx.doi.org/10.1094/PDIS-02-18-0261-PDNDOI Listing
September 2018

Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon.

IMA Fungus 2018 Jun 28;9(1):177-183. Epub 2018 May 28.

Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.

The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048572PMC
June 2018