Phylogenetic lineages in Entomophthoromycota

Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Case report: Localized coloproctitis caused by novel Basidiobolus arizonensis in a dog

A 6-year-old male neutered boxer mix canine was presented for a one-month history of dyschezia, hematochezia, and constipation. Colonoscopy and endoscopic biopsies revealed non-specific lymphoplasmacytic, eosinophilic colitis. Despite pursuing various therapies over a 3.5-month clinical course (including hypoallergenic diet, antibiotics, prokinetics, laxatives, and anti-inflammatory glucocorticoids), the patient's condition did not improve. Two and a half months after initial presentation, the patient developed circumferential proctitis with multiple draining tracts and obstipation. Humane euthanasia and postmortem examination were elected. Gross and histological findings revealed locally extensive pyogranulomatous coloproctitis with many intralesional PAS-positive, GMS-negative 30-40 μm in diameter, hyaline, pauciseptate, irregularly branching fungal hyphae, hyphal bodies or chlamydospores and 25-45 μm in diameter thick-walled zygospores. Fungal culture of fluid from the draining tracts was performed, and DNA sequence analysis of the ITS and partial LSU of the nuclear ribosomal RNA genes were used to identify and confirm a novel species, Basidiobolus arizonensis. Basidiobolus spp. are saprobes in the order Basidiobolales and most commonly cause granulomatous infections of the skin, respiratory tract, and gastrointestinal tract in veterinary species and humans. To the authors' knowledge, this is the first report of novel Basidiobolus arizonensis causing localized coloproctitis in a dog.

Discovery and genomic characterization of three double-stranded RNA viruses coinfecting Conidiobolus taihushanensis

Conidiobolus sensu lato, a genus within the family Ancylistaceae, encompasses a diverse range of fungal species that are widely distributed in plant debris and soil. In this study, we identified three double-stranded RNA (dsRNA) viruses coinfecting a strain of Conidiobolus taihushanensis. These viruses were identified as Conidiobolus taihushanensis totivirus 1 (CtTV1), Conidiobolus nonsegmented RNA virus 1-2 (CNRV1-2), and Conidiobolus taihushanensis virus 1 (CtV1). Through high-throughput sequencing and RNA-ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we determined their complete genome sequences. The genome of CtTV1 is 6,921 nucleotides in length, containing two open reading frames (ORFs). ORF1 encodes a 1,124-amino-acid capsid protein (CP) with a molecular weight of 125.07 kDa, and ORF2 encodes a 780-amino-acid RNA-dependent RNA polymerase (RdRp) with a molecular weight of 88.05 kDa. CNRV1-2, approximately 3.0 kb in length, also contains two ORFs, which are predicted to encode a 186-amino-acid hypothetical protein (HP) and a 758-amino-acid RdRp. CtV1 has a smaller genome consisting of 3,081 base pairs (bp) with two ORFs: one encoding a 244-amino-acid HP (26.85 kDa) and the other encoding a 707-amino-acid RdRp (80.64 kDa). Phylogenetic analysis based on RdRp sequences revealed that CtTV1 shows the highest similarity to Phytophthora pluvialis RNA virus 1, with 38.79% sequence identity, and clusters with members of the family Orthototiviridae, and it is most closely related to Utsjoki toti-like virus. In contrast, CtV1 formed a unique branch and might represent a new genus. The genome sequence of CNRV1-2 is 99.74% identical to that of the previously described Conidiobolus non-segmented RNA virus 1 (CNRV1). Our findings indicate that CtTV1 and CtV1 are distinct novel viruses, while CNRV1-2 appears to be a variant of CNRV1. This study enhances our understanding of the genetic diversity and evolutionary relationships among mycoviruses associated with C. taihushanensis.

SCHIZANGIELLA INFECTIONS IN AN EASTERN RATSNAKE (PANTHEROPHIS ALLEGHANIENSIS) AND A TIMBER RATTLESNAKE (CROTALUS HORRIDUS)

This report describes Schizangiella infections in colubrid and viperid snakes. A captive eastern ratsnake (Pantherophis alleghaniensis) was presented for a large intraoral mass associated with the mandible. The mass was debulked and histologic examination revealed severe, granulomatous stomatitis with intralesional fungi exhibiting morphologic features consistent with Schizangiella serpentis. PCR and sequencing of affected tissues confirmed S. serpentis. Because of declining health, the ratsnake was euthanized and postmortem examination identified a disseminated S. serpentis infection involving the skeletal musculature, lung, kidney, mesentery, and mandible. A wild-caught timber rattlesnake (Crotalus horridus) was presented for cutaneous lesions, weakness, and lethargy and later died. Postmortem examination revealed a mass-like structure in the esophagus characterized by high numbers of Schizangiella-like fungi associated with extensive granulomatous inflammation; the snake also had cutaneous mycosis suggestive of ophidiomycosis. This is the first report to document the unique morphologic features of S. serpentis in tissues and the presentation of schizangiellosis in snakes. Schizangiellosis should be considered as a differential diagnosis for nodular lesions involving the oral cavity and/or the gastrointestinal tract of snakes.

Unveiling species diversity within the family Conidiobolaceae (Entomophthorales) in China: Descriptions of two new species and reassessment of the taxonomic position of Conidioboluspolyspermus

In the present study, two new Conidiobolus s.s. species were described relying on the morphological studies and phylogenetic analysis utilizing nuclear large subunit of rDNA (nucLSU), mitochondrial small subunit of rDNA (mtSSU), and elongation-factor-like gene (EFL) sequences. Conidiobolusjiangxiensissp. nov. is distinguished by its short primary conidiophores, a feature not commonly observed in other Conidiobolus s.s. species. Conversely, Conidiobolusmarcoconidiussp. nov. is characterized by larger primary conidia and the emergence of 2-5 secondary conidia from each branched secondary conidiophores. Additionally, the taxonomic reassessment of C.polyspermus confirms its distinct status within the genus Conidiobolus s.s. Moreover, molecular analyses, incorporating the nucLSU, mtSSU, and EFL sequences, provide robust support for the phylogenetic placement of the two newly described species and the taxonomic identity of C.polyspermus. This investigation contributes valuable insights into the species diversity of Conidiobolaceae in China, enhancing our understanding of the taxonomy within this fungal family.

Pandora cacopsyllae Eilenberg, Keller & Humber (Entomophthorales: Entomophthoraceae), a new species infecting pear psyllid Cacopsylla pyri L. (Hemiptera: Psyllidae)

The new species Pandora cacopsyllae Eilenberg, Keller & Humber (Entomophthorales) is described. The fungus was found on infected pear psyllids Cacopsylla pyri (Hemiptera: Psyllidae) in a pear orchard in Zealand, Denmark. Morphological structures (conidia, rhizoids, cystidia) were described on the designated type host C. pyri. In addition, conidia from an in vitro culture were described. Pandora cacopsyllae differs from other Pandora species by a) C. pyri is the natural host; b) conidia are different from other Pandora species infecting Psylloidea; c) ITS differs from other Pandora species infecting Hemiptera. The fungus has a high potential for future use in biological control of Cacopsylla pest species as well as other psyllids.

Fungal taxonomy: A puzzle with many missing pieces

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Diversity and Breadth of Host Specificity among Arthropod Pathogens in the Entomophthoromycotina

A meta-analysis based on the published literature was conducted to evaluate the breadth of host ranges of arthropod pathogens in the fungal subphylum Entomophthoromycotina. The majority of pathogens in this subphylum infect insects, although arachnids (especially mites), collembola, and myriapods are also used as hosts. Most species (76%) have specialized host ranges and only infect arthropods in one host family. The breadth of host ranges in the Entomophthoromycotina is generally greater for species in more basal groups (Conidiobolaceae and Neoconidiobolaceae), where most species are soil-borne saprobes and few are pathogens. The Batkoaceae is a transitionary family in which all species are pathogens and both generalists and specialists occur. Among pathogen-infecting insects, Hemiptera and Diptera are the most commonly infected insect orders. Within the Hemiptera, hosts in the suborder Sternorrhycha were infected by more fungal species than the Auchenorrhyncha and Heteroptera.

Batkoa major infecting the invasive planthopper Lycorma delicatula

The entomopathogenic fungi Batkoa major and Beauveria bassiana caused co-epizootics in populations of invasive spotted lanternflies, Lycorma delicatula, in 2018 in northeastern North America. Although first described from North America in 1888, the biology and ecology of Batkoa major had not been studied since that time. This entomophthoralean fungus found infecting L. delicatula in 2018 produces conidia and rhizoids similar in appearance to the original description. We conducted laboratory bioassays to investigate infection of different ages and sexes of these planthoppers, inoculating via showered conidia. All nymphs, and male and female adults were susceptible to infection. Adult males died more quickly than adult females or fourth instars. Batkoa major grew out of cadavers of adult males more frequently than adult females or fourth instar nymphs. Rhizoids that provide attachment of cadavers to substrates were produced from adult cadavers more frequently than conidia. Resting spores were not observed in vivo or in vitro in the lab, or in the field.

Potential Impact of Chemical Fungicides on the Efficacy of Metarhizium rileyi and the Occurrence of Pandora gammae on Caterpillars in Soybean Crops

Entomopathogenic fungi may play a crucial role in the regulation of caterpillar populations in soybean crops, either through natural occurrences or applied as mycopesticides. In the present work, we reported the naturally occurring entomopathogenic fungus Pandora gammae attacking the caterpillar Chrysodeixis includens, with infection rates in field trials ran in two consecutive years in the 10-35% range. As many chemicals are potentially harmful to entomopathogenic fungi, this work aimed to investigate the potential impact of two chemical fungicides (azoxystrobin + benzovindiflupyr and trifloxistrobina + prothioconazole) used to control soybean rust (Phakopsora pachyrhizi) on the natural occurrence of P. gammae and Metarhizium rileyi, as well as the efficacy of the latter fungus applied as different formulations against the soybean caterpillars Anticarsia gemmatalis and C. includens. Under laboratory conditions, fungicides used at field-recommended rates had a considerable negative impact on the germinability of M. riley on the medium surface, and all tested formulations did not protect conidia from damage by these chemicals. This harmful effect also impacted host infectivity, as the larval mortality owing to this fungus was reduced by 30-40% compared to that of the fungicide-free treatments. In field trials conducted in two subsequent years, unformulated and formulated M. rileyi conidia applied to soybean plants produced primary infection sites in caterpillar populations after a single spray. Spraying unformulated or formulated M. rileyi conidia following fungicide application on plants did not affect host infection rates over time. Moreover, the use of M. rileyi-based formulations or chemical fungicide did not interfere with the natural infection rates by P. gammae on its host, C. includens. Although a higher degree of exposure to non-selective fungicides can negatively affect fungal entomopathogens, a single foliar application of fungicides may be harmless to both M. rileyi and P. gammae in soybean fields. Additionally, this work showed that naturally occurring wasps and tachnids also play an important role in the regulation of A. gemmatalis and, notably, C. includens, with parasitism rates above 40-50% in some cases.

The Early Terrestrial Fungal Lineage of Conidiobolus-Transition from Saprotroph to Parasitic Lifestyle

Fungi of the Conidiobolus group belong to the family Ancylistaceae (Entomophthorales, Entomophthoromycotina, Zoopagomycota) and include over 70 predominantly saprotrophic species in four similar and closely related genera, that were separated phylogenetically recently. Entomopathogenic fungi of the genus Batkoa are very close morphologically to the Conidiobolus species. Their thalli share similar morphology, and they produce ballistic conidia like closely related entomopathogenic Entomophthoraceae. Ballistic conidia are traditionally considered as an efficient tool in the pathogenic process and an important adaptation to the parasitic lifestyle. Our study aims to reconstruct the phylogeny of this fungal group using molecular and genomic data, ancestral lifestyle and morphological features of the conidiobolus-like group and the direction of their evolution. Based on phylogenetic analysis, some species previously in the family Conidiobolaceae are placed in the new families Capillidiaceae and Neoconidiobolaceae, which each include one genus, and the Conidiobolaceae now includes three genera. Intermediate between the conidiobolus-like groups and Entomophthoraceae, species in the distinct Batkoa clade now belong in the family Batkoaceae. Parasitism evolved several times in the Conidiobolus group and Ancestral State Reconstruction suggests that the evolution of ballistic conidia preceded the evolution of the parasitic lifestyle.

Season-long infection of diverse hosts by the entomopathogenic fungus Batkoa major

Populations of the entomopathogenic fungus Batkoa major were analyzed using sequences of four genomic regions and evaluated in relation to their genetic diversity, insect hosts and collection site. This entomophthoralean pathogen killed numerous insect species from 23 families and five orders in two remote locations during 2019. The host list of this biotrophic pathogen contains flies, true bugs, butterflies and moths, beetles, and barkflies. Among the infected bugs (Order Hemiptera), the spotted lanternfly (Lycorma delicatula) is a new invasive planthopper pest of various woody plants that was introduced to the USA from Eastern Asia. A high degree of clonality occurred in the studied populations and high gene flow was revealed using four molecular loci for the analysis of population structure. We did not detect any segregation in the population regarding host affiliation (by family or order), or collection site. This is the first description of population structure of a biotrophic fungus-generalist in the entomopathogenic Order Entomophthorales. This analysis aimed to better understand the potential populations of entomopathogen-generalists infecting emerging invasive hosts in new ecosystems.

Two new species in Capillidium (Ancylistaceae, Entomophthorales) from China, with a proposal for a new combination

A taxonomic revision of Conidiobolus s.l. (Ancylistaceae, Entomophthorales) delimited all members that form capilliconidia into the genus Capillidium. In this study, we report two new species of Capillidium that were isolated in China. Capillidiummacrocapilliconidium sp. nov. is characterised by large capilliconidia. Capillidiumjiangsuense sp. nov. is differentiated by large capilliconidia and long, slender secondary conidiophores. Phylogenetic analyses were performed using sequences from the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU) and elongation-factor-like (EFL). The analyses revealed sister relationships between Ca.macrocapilliconidium sp. nov. and Ca.globuliferus / Ca.pumilum and between Ca.jiangsuense sp. nov. and Ca.denaeosporum. Additionally, a new combination of Ca.rugosum (Drechsler) B. Huang & Y. Nie comb. nov. is proposed herein. An identification key is provided for the ten accepted Capillidium species.

 Azygosporus gen. nov., a synapmorphic clade in the family Ancylistaceae

The fungal genus Conidiobolus sensu lato was delimited into four genera based on morphology and phylogeny. However, the taxonomic placement of C.parvus has not been determined until now. Here, we show that C.parvus belongs to a distinct lineage based on mitochondrial (mtSSU) and nuclear (TEF1 and nrLSU) phylogenetic analyses. Phylogenetic analyses further revealed a new species as sister to C.parvus. We identified a synapomorphy uniting these lineages (azygospore production) that was not observed in other allied genera of the family Ancylistaceae, and erected a new genus Azygosporusgen. nov. for this monophyletic group, with a new combination, A.parvuscomb. nov. as the type species. Within Azygosporus, the novel species A.macropapillatussp. nov. was introduced from China based on morphological characteristics and molecular evidence, which is characterized by its prominent basal papilla, in comparison to other closely related species, measuring 7.5–10.0×5.0–10.0 µm. Our study resolved the phylogenetic placement of C.parvus and improved the taxonomic system of the Ancylistaceae family.

First report on the natural occurrence of entomopathogenic fungi in populations of the leafhopper Dalbulus maidis (Hemiptera: Cicadellidae): Pathogen identifications and their incidence in maize crops

The corn leafhopper Dalbulus maidis is one of the most important pests of maize in Latin America. Here we report, for the first time, the natural occurrence of two fungal species infecting the adult stage of this pest. In 2020, insects killed by a pale bluish green fungus in irrigated maize fields located in Northeast Brazil were found attached to the abaxial surface of leaves. Using morphological characters and multigenic phylogeny, it was identified as Metarhizium brasiliense. In the beginning of 2021, the same pathogen was seen on adults in a maize field in the Central-Western region, alongside an entomophthoralean fungus during an epizootic. The latter pathogen was molecularly identified as a species in the genus Batkoa. The number of Batkoa-infected leafhoppers, displaying the typical swollen abdomen and extended wings, reached an average of 1.88 per maize leaf (86.42% of the sampled adults). The incidence of M. brasiliense was higher in plots in the Northeastern region (0.22 and 0.53 adult per leaf) when compared to the Central-Western region (0.04 adult per leaf). The report of D. maidis adults infected by M. brasiliense in agricultural settings located in different geographic regions and over 550 km apart indicates probable widespread occurrence of this pathogen in Brazil. Moreover, this opens the possibility of more applied biological control studies and, perhaps, the development of new tools to manage D. maidis populations.

The genus Entomophthora: bringing the insect destroyers into the twenty-first century

The fungal genus Entomophthora consists of highly host-specific pathogens that cause deadly epizootics in their various insect hosts. The most well-known among these is the "zombie fly" fungus E. muscae, which, like other Entomophthora species, elicits a series of dramatic behaviors in infected hosts to promote optimal spore dispersal. Despite having been first described more than 160 years ago, there are still many open questions about Entomophthora biology, including the molecular underpinnings of host behavior manipulation and host specificity. This review provides a comprehensive overview of our current understanding of the biology of Entomophthora fungi and enumerates the most pressing outstanding questions that should be addressed in the field. We briefly review the discovery of Entomophthora and provide a summary of the 21 recognized Entomophthora species, including their type hosts, methods of transmission (ejection of spores after or before host death), and for which molecular data are available. Further, we argue that this genus is globally distributed, based on a compilation of Entomophthora records in the literature and in online naturalist databases, and likely to contain additional species. Evidence for strain-level specificity of hosts is summarized and directly compared to phylogenies of Entomophthora and the class Insecta. A detailed description of Entomophthora's life-cycle and observed manipulated behaviors is provided and used to summarize a consensus for ideal growth conditions. We discuss evidence for Entomophthora's adaptation to growth exclusively inside insects, such as producing wall-less hyphal bodies and a unique set of subtilisin-like proteases to penetrate the insect cuticle. However, we are only starting to understand the functions of unusual molecular and genomic characteristics, such as having large > 1 Gb genomes full of repetitive elements and potential functional diploidy. We argue that the high host-specificity and obligate life-style of most Entomophthora species provides ample scope for having been shaped by close coevolution with insects despite the current general lack of such evidence. Finally, we propose six major directions for future Entomophthora research and in doing so hope to provide a foundation for future studies of these fungi and their interaction with insects.

The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus

The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.

Strongwellsea crypta (Entomophthorales: Entomophthoraceae), a new species infecting Botanophila fugax (Diptera: Anthomyiidae)

A new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) is described: Strongwellsea crypta Eilenberg & Humber from adult Botanophila fugax (Meigen) (Diptera: Anthomyiidae). The description is based on pathobiological, phenotypical and genotypical characters. The abdominal holes in infected hosts develop rapidly and become strikingly large and edgy, almost rhomboid in shape. The new species S. crypta differs from S. castrans, the only described species infecting flies from Anthomyiidae, by: (a) naturally infecting another host species, (b) by having significantly longer primary conidia, and (c) by genotypical clustering separately from that species when sequencing ITS2.

Basidiobolus omanensis sp. nov. Causing Angioinvasive Abdominal Basidiobolomycosis

Human infectious fungal diseases are increasing, despite improved hygienic conditions. We present a case of gastrointestinal basidiobolomycosis (GIB) in a 20-year-old male with a history of progressively worsening abdominal pain. The causative agent was identified as a novel Basidiobolus species. Validation of its novelty was established by analysis of the partial ribosomal operon of two isolates from different organs. Phylogeny of ITS and LSU rRNA showed that these isolates belonged to the genus Basidiobolus, positioned closely to B. heterosporus and B. minor. Morphological and physiological data supported the identity of the species, which was named Basidiobolus omanensis, with CBS 146281 as the holotype. The strains showed high minimum inhibitory concentrations (MICs) to fluconazole (>64 µg/mL), itraconazole and voriconazole (>16 µg/mL), anidulafungin and micafungin (>16 µg/mL), but had a low MIC to amphotericin B (1 µg/mL). The pathogenic role of B. omanensis in gastrointestinal disease is discussed. We highlight the crucial role of molecular identification of these rarely encountered opportunistic fungi.

Insects and their pathogens in a changing climate

The complex nature of climate change-mediated multitrophic interaction is an underexplored area, but has the potential to dramatically shift transmission and distribution of many insects and their pathogens, placing some populations closer to the brink of extinction. However, for individual insect-pathogen interactions climate change will have complicated hard-to-anticipate impacts. Thus, both pathogen virulence and insect host immunity are intrinsically linked with generalized stress responses, and in both pathogen and host have extensive trade-offs with nutrition (e.g., host plant quality), growth and reproduction. Potentially alleviating or exasperating these impacts, some pathogens and hosts respond genetically and rapidly to environmental shifts. This review identifies many areas for future research including a particular need to identify how altered global warming interacts with other environmental changes and stressors, and how consistent these impacts are across pathogens and hosts. With that achieved we would be closer to producing an overarching framework to integrate knowledge on all environmental interplay and infectious disease events.

A genome-scale phylogeny of the kingdom Fungi

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

Differentiation of Basidiobolus spp. Isolates: RFLP of a Diagnostic PCR Amplicon Matches Sequence-Based Classification and Growth Temperature Preferences

The genus Basidiobolus, known since 1886, is primarily associated with reptiles and amphibians. Although globally distributed, rare infections caused by members of this genus mainly occur in tropical and subtropical regions. Morphological and physiological characteristics were used in the past for the description of species. However, some of these characteristics vary depending on culture conditions. Therefore, most species names are regarded as synonyms of B. ranarum as the only pathogenic species. Yet, not all environmental isolates are necessarily pathogenic. This study aimed to analyze if environmental Basidiobolus isolates can be distinguished reliably based on morpho-physiological and molecular characteristics. Eleven isolates originally obtained from feces of south African reptiles and one type strain, Basidiobolus microsporus DSM 3120, were examined morpho-physiologically. Sequence analysis of the 18S and partial 28S rRNA gene and restriction analysis of a diagnostic amplicon (restriction fragment length polymorphism, RFLP) were performed for all 12 strains. Based on the results obtained, morphological features and the 18S rRNA sequence proved insufficient for the reliable differentiation of isolates. However, isolates were distinguishable by growth temperature profiles, which matched isolate clusters established by partial 28S rRNA gene sequence and restriction analysis of a Basidiobolus specific diagnostic PCR amplicon. Our results indicate that RFLP analysis can be used as a fast screening method to identify Basidiobolus isolates with similar physiological characteristics.

Morphological and Molecular Characterization of Entomophthorales (Entomophthoromycota: Entomophthoromycotina) from Argentina

We characterized 17 insect-pathogenic entomophthoralean fungal isolates (Entomophthoromycotina: Entomophthorales) using morphological and molecular techniques. We identified four species from various insect hosts: (<strong><em>i</em></strong>) <em>Entomophthora planchoniana</em>, six specimens from aphids; (<strong><em>ii</em></strong>) <em>Pandora </em><em>neoaphidis</em>, three specimens from aphids; (<strong><em>iii</em></strong>) <em>Zoophthora phalloides </em>from an aphid; and (<strong><em>iv</em></strong>) <em>Z. radicans</em>, seven specimens from insects in the orders Diptera, Hemiptera, and Lepidoptera. Analysis of ITS1 data from <em>E. planchoniana </em>showed clustering in accordance to aphid host species. <em>Entomophthora planchoniana </em>from <em>Macrosiphum</em><em> </em><em>euphorbiae </em>clustered together, separate from the isolate from <em>Myzus persicae</em>. The <em>P.</em><em> </em><em>neoaphidis </em>specimens clustered with sequences from other aphid-pathogenic <em>Pandora </em>species in GenBank. In this study, <em>Z. phalloides </em>from <em>Brevicoryne brassicae </em>and <em>Z. radicans </em>from an unidentified species of Chironomidae (Diptera) in Argentina were characterized for the first time. The present study was initiated to elucidate the taxonomy of the entomophthoralean fungi in Argentina according to their morphological and molecular characters. The presented results emphasize the significance of the combination of molecular data and information on morphology, ecology, and host range for accurate identification of entomophthoralean and allied genera.

Conidiobolus lunulus, a new entomophthoralean species isolated from leafcutter ants

Entomophthoralean fungi with pathogenic abilities to infect social insects are rare. Here, we describe a fungus isolated from leafcutter ants. Morphologically, the fungus has spherical primary conidia and two types of microconidia: one with the same shape as the primary conidia and another with an elliptical to half-moon shape. The fungus also produces villose conidia known previously only from Conidiobolus coronatus. A multilocus phylogenetic analysis was performed with nuc rDNA sequences from three regions (28S, 18S, and internal transcribed spacer [ITS]). Our isolates are distinguished as a new species, described here as Conidiobolus lunulus, and is more closely related to C. brefeldianus than to C. coronatus, despite the greater morphological resemblance to the latter. Morphological differences, unique phylogenetic placement, and isolation from an altogether new host support this finding. This is the first record of an entomophthoralean species isolated from leafcutter ants.

Three new species of Conidiobolus sensu stricto from plant debris in eastern China

The genus Conidiobolus Bref. is widely distributed and the Conidiobolus sensu lato contained three other genera, Capillidium, Microconidiobolus and Neoconidiobolus. A molecular phylogeny based on the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU) and the translation elongation factor 1-alpha gene (TEF1) revealed three novel species within the clade of Conidiobolus s.s., i.e. C. bifurcatus sp. nov., C. taihushanensis sp. nov. and C. variabilis sp. nov. These three species were isolated from plant debris in eastern China. Morphologically, C. bifurcatus sp. nov. is characterised by its secondary conidiophores often branched at the tip to form two short stipes each bearing a secondary conidium. C. taihushanensis sp. nov. is different from the others in its straight apical mycelia and the production of 2-5 conidia. C. variabilis sp. nov. is distinctive because of its various shapes of primary conidia. All these three new taxa are illustrated herein with an update key to the species of the genus Conidiobolus s.s.

Conidiobolomycosis, cryptococcosis, and aspergillosis in sheep and goats: a review

We review herein infections by Conidiobolus spp., Cryptococcus spp., and Aspergillus spp. in sheep and goats. Conidiobolus spp. are common causes of rhinitis in sheep and are less frequent in goats, in which Conidiobolus spp. also cause skin lesions. Cryptococcus spp. cause rhinitis, meningitis, encephalitis, and pneumonia in goats, and are rarely observed in sheep. Aspergillus spp. may cause rhinitis in goats, and pneumonia and mastitis in sheep and goats. Gross and microscopic lesions caused by these 3 fungal infections may be similar to each other. The diagnosis of these diseases must be based on gross and microscopic lesions, coupled with detection of the agent by immunohistochemical, molecular, and/or culture-based methods.

Strongwellsea tigrinae and Strongwellsea acerosa (Entomophthorales: Entomophthoraceae), two new species infecting dipteran hosts from the genus Coenosia (Muscidae)

Two new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) are described: Strongwellsea tigrinae from adult Coenosia tigrina (Diptera: Muscidae) and Strongwellsea acerosa from adult Coenosia testacea. The descriptions are based on pathobiological, phenotypical and genotypical characters. Further, the circumscription of the genus Strongwellsea is emended. Our findings suggest that Strongwellsea harbors a high number of species, of which now only five have been described.

Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

The fungal genus Massospora (Zoopagomycota: Entomophthorales) includes more than a dozen obligate, sexually transmissible pathogenic species that infect cicadas (Hemiptera) worldwide. At least two species are known to produce psychoactive compounds during infection, which has garnered considerable interest for this enigmatic genus. As with many Entomophthorales, the evolutionary relationships and host associations of Massospora spp. are not well understood. The acquisition of M. diceroproctae from Arizona, M. tettigatis from Chile, and M. platypediae from California and Colorado provided an opportunity to conduct molecular phylogenetic analyses and morphological studies to investigate whether these fungi represent a monophyletic group and delimit species boundaries. In a three-locus phylogenetic analysis including the D1-D2 domains of the nuclear 28S rRNA gene (28S), elongation factor 1 alpha-like (EFL), and beta-tubulin (BTUB), Massospora was resolved in a strongly supported monophyletic group containing four well-supported genealogically exclusive lineages, based on two of three methods of phylogenetic inference. There was incongruence among the single-gene trees: two methods of phylogenetic inference recovered trees with either the same topology as the three-gene concatenated tree (EFL) or a basal polytomy (28S, BTUB). Massospora levispora and M. platypediae isolates formed a single lineage in all analyses and are synonymized here as M. levispora. Massospora diceroproctae was sister to M. cicadina in all three single-gene trees and on an extremely long branch relative to the other Massospora, and even the outgroup taxa, which may reflect an accelerated rate of molecular evolution and/or incomplete taxon sampling. The results of the morphological study presented here indicate that spore measurements may not be phylogenetically or diagnostically informative. Despite recent advances in understanding the ecology of Massospora, much about its host range and diversity remains unexplored. The emerging phylogenetic framework can provide a foundation for exploring coevolutionary relationships with cicada hosts and the evolution of behavior-altering compounds.

A taxonomic revision of the genus Conidiobolus (Ancylistaceae, Entomophthorales): four clades including three new genera

The genus Conidiobolus is an important group in entomophthoroid fungi and is considered to be polyphyletic in recent molecular phylogenies. To re-evaluate and delimit this genus, multi-locus phylogenetic analyses were performed using the large and small subunits of nuclear ribosomal DNA (nucLSU and nucSSU), the small subunit of the mitochondrial ribosomal DNA (mtSSU) and the translation elongation factor 1-alpha (EF-1α). The results indicated that the Conidiobolus is not monophyletic, being grouped into a paraphyletic grade with four clades. Consequently, the well-known Conidiobolus is revised and three new genera Capillidium, Microconidiobolus and Neoconidiobolus are proposed along with one new record and 22 new combinations. In addition, the genus Basidiobolus is found to be basal to the other entomophthoroid taxa and the genus Batkoa locates in the Entomophthoraceae clade.

Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis

Basidiobolus species were isolated from colonic biopsy samples of patients with gastrointestinal basidiobolomycosis (GIB) in southern Saudi Arabia. Isolated fungi were initially identified using classical mycological tools and confirmed by sequence analysis of the large subunit ribosomal RNA gene. Phenotypic tests revealed zygomycete-like fungi which conform to those of Basidiobolus species. Five sequenced strains formed a monophyletic clade in the 28S ribosomal RNA gene phylogenetic tree. They shared 99.97% similarity with B. haptosporus and 99.97% with B. haptosporus var. minor, and relatively lower similarity with B. ranarum (99.925%). The study suggests a new and a serious causal agent of GIB related to Basidiobolus haptosporus. These isolates are not related to B. ranarum, which is commonly linked to this disease.

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.

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.

First-time isolation and quantification of Basidiobolus spp. from reptile faeces in KwaZulu-Natal (South Africa) using selective media

Members of the genus Basidiobolus are potentially pathogenic fungi, known to cause mycoses in tropical and subtropical countries. Basidiobolus spp. can be associated with animals, and reptiles and amphibians are candidate vectors for the distribution of this fungus. The presence of Basidiobolus spp. was described for different reptiles in several African countries, although not for South Africa. In addition, quantitative data are scarce. The aim of this study was to analyse faeces of selected South African reptiles for the presence and quantity of "viable Basidiobolus units." Faecal samples of gecko and agama lizards were collected and analysed using spread plating, with confirmation by PCR. The addition of dichloran and benomyl to standard fungal media improved the selectivity and allowed quantification of Basidiobolus spp. in reptile faeces. The amount of Basidiobolus spp. varied between 300 and 1.4 × 106  CFU per gram of pooled gecko faeces, which mostly corresponds to >1000 CFU per outside dropping and <100 CFU per inside dropping. About 60% of analysed agama faeces carried Basidiobolus spp., ranging from 150 to 1.2 × 105  CFU per dropping. Our results show for the first time that faeces of South African reptiles frequently carry Basidiobolus spp., confirming that they can contribute to the distribution of this fungus.

Gastrointestinal basidiobolomycosis: An emerging mycosis difficult to diagnose but curable. Case report and review of the literature

BACKGROUND

Gastrointestinal basidiobolomycosis (GIB) is a rare mycosis affecting almost exclusively immunocompetent subjects.

METHODS

We describe a case of GIB caused by Basidiobolus ranarum in a 25-year-old Italian immunocompetent man resident in Ireland who presented a 2-month history of epigastric pain. Suspecting colon cancer he underwent a right hemicolectomy subsequently leading to a diagnosis of GIB by means of molecular biology. After surgery a 9-month therapy with itraconazole was employed with a good outcome. A review of medical literature regarding GIB cases published in the period 1964-2017 is presented.

RESULTS

One-hundred and two cases of GIB were included in this analysis. The disease was observed predominantly in male gender (74.5%) and children (41.2%). Abdominal pain was the single most common complaint (86.3%) followed by fever (40.2%) and evidence of an abdominal mass (30.4%). Peripheral blood eosinophilia was detected in 85.7% of cases. Most of the patients were diagnosed in Saudi Arabia (37.2%) followed by USA (21.6%) and Iran (20.6%). Surgery plus antifungal therapy was employed in the majority of patients (77.5%). An unfavourable outcome was documented globally in 18.6% of patients.

CONCLUSIONS

GIB seems to be an emerging intestinal mycosis among immunocompetent patients living in the Middle East and Arizona.

Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi

Entomophthoroid fungi represent an ecologically important group of fungal pathogens on insects. Here, the whole mitogenome of Conidiobolus heterosporus, one of the entomophthoroid fungi, was described and compared to those early branching fungi with available mitogenomes. The 53,364-bp circular mitogenome of C. heterosporus contained two rRNA genes, 14 standard protein-coding genes, 26 tRNA genes, and three free-standing ORFs. Thirty introns interrupted nine mitochondrial genes. Phylogenetic analysis based on mitochondrion-encoded proteins revealed that C. heterosporus was most close to Zancudomyces culisetae in the Zoopagomycota of basal fungi. Comparison on mitogenomes of 23 basal fungi revealed great variabilities in terms of mitogenome conformation (circular or linear), genetic code (codes 1, 4, or 16), AT contents (53.3-85.5%), etc. These mitogenomes varied from 12.0 to 97.3 kb in sizes, mainly due to different numbers of genes and introns. They showed frequent DNA rearrangement events and a high variability of gene order, although high synteny and conserved gene order were also present between closely related species. By reporting the first mitogenome in Entomophthoromycotina and the second in Zoopagomycota, this study greatly enhanced our understanding on evolution of basal fungi.

Human Pathogenic Entomophthorales

The pathogenic entomophthoralean fungi cause infection in insects and mammalian hosts. Basidiobolus and Conidiobolus species can be found in soil and insect, reptile, and amphibian droppings in tropical and subtropical areas. The life cycles of these fungi occur in these environments where infecting sticky conidia are developed. The infection is acquired by insect bite or contact with contaminated environments through open skin. Conidiobolus coronatus typically causes chronic rhinofacial disease in immunocompetent hosts, whereas some Conidiobolus species can be found in immunocompromised patients. Basidiobolus ranarum infection is restricted to subcutaneous tissues but may be involved in intestinal and disseminated infections. Its early diagnosis remains challenging due to clinical similarities to other intestinal diseases. Infected tissues characteristically display eosinophilic granulomas with the Splendore-Höeppli phenomenon. However, in immunocompromised patients, the above-mentioned inflammatory reaction is absent. Laboratory diagnosis includes wet mount, culture serological assays, and molecular methodologies. The management of entomophthoralean fungi relies on traditional antifungal therapies, such as potassium iodide (KI), amphotericin B, itraconazole, and ketoconazole, and surgery. These species are intrinsically resistant to some antifungals, prompting physicians to experiment with combinations of therapies. Research is needed to investigate the immunology of entomophthoralean fungi in infected hosts. The absence of an animal model and lack of funding severely limit research on these fungi.

Sleeping Beauties: Horizontal Transmission via Resting Spores of Species in the Entomophthoromycotina

Many of the almost 300 species of arthropod-pathogenic fungi in the Entomophthoromycotina (Zoopagomycota) are known for being quite host-specific and are able to cause epizootics. Most species produce two main types of spores, conidia and resting spores. Here, we present a review of the epizootiology of species of Entomophthoromycotina, focusing on their resting spores, and how this stage leads to horizontal transmission and persistence. Cadavers in which resting spores are produced can often be found in different locations than cadavers of the same host producing conidia. Resting spores generally are dormant directly after production and require specific conditions for germination. Fungal reproduction resulting from infections initiated by Entomophaga maimaiga resting spores can differ from reproduction resulting from conidial infections, although we do not know how commonly this occurs. Reservoirs of resting spores can germinate for variable lengths of time, including up to several months, providing primary infections to initiate secondary cycling based on conidial infections, and not all resting spores germinate every year. Molecular methods have been developed to improve environmental quantification of resting spores, which can exist at high titers after epizootics. Ecological studies of biological communities have demonstrated that this source of these spores providing primary inoculum in the environment can decrease not only because of germination, but also because of the activity of mycopathogens.

Variation in physiological host range in three strains of two species of the entomopathogenic fungus Beauveria

Knowledge of the host range of a biocontrol agent (BCA) is fundamental. Host range determines the BCA's economic potential, as well as the possible risk for non-target organisms. Entomopathogenic fungal strains belonging to the genus Beauveria are widely used as BCA, but our knowledge of their physiological host range is only partial. The aim of this study was to improve our understanding of the physiological host range of three Beauveria strains belonging to two species, B. hoplocheli and B. bassiana. We performed laboratory mortality bioassays to assess their pathogenicity and virulence against nine insect pests, belonging to three orders: Lepidoptera, Coleoptera and Diptera. Mortality rate, mean survival time and mycosis rate were used to estimate virulence. Pathogenicity was assessed as the capacity to cause a disease and induce mortality. Virulence was assessed as the severity of the disease based on mortality rate, mean survival time and mycosis rate. The results of this study revealed significant differences in the physiological host range of the three Beauveria strains tested. The three strains were pathogenic to all Diptera and Lepidoptera species tested. In the case of the Coleoptera, only the B. hoplocheli strain was pathogenic to the white grub Hoplochelus marginalis and only the B. bassiana strains were pathogenic to Alphitobius diaperinus. The B. hoplocheli strain was less virulent on Lepidoptera and Diptera than the two B. bassiana strains. The latter both exhibited very similar virulence patterns. The fact that B. hoplocheli and B. bassiana strains have different host ranges means that they can be used as BCA to target different pests. Impacts on non-target insects across multiple orders cannot be ruled out in the absence of ecological host range studies.

Subcutaneous Granulomatous Inflammation due to Basidiobolomycosis: Case Reports of 3 Patients in Buruli Ulcer Endemic Areas in Benin

BACKGROUND

Basidiobolomycosis is a rare subcutaneous mycosis, which can be mistaken for several other diseases, such as soft tissue tumors, lymphoma, or Buruli ulcer in the preulcerative stage. Microbiological confirmation by PCR for Basidiobolus ranarum and culture yield the most specific diagnosis, yet they are not widely available in endemic areas and with varying sensitivity. A combination of histopathological findings, namely, granulomatous inflammation with giant cells, septate hyphal fragments, and the Splendore-Hoeppli phenomenon, can confirm basidiobolomycosis in patients presenting with painless, hard induration of soft tissue.

CASE PRESENTATIONS

We report on three patients misdiagnosed as suffering from Buruli ulcer, who did not respond to Buruli treatment. Histopathological review of the tissue sections from these patients suggests basidiobolomycosis. All patients had been lost to follow-up, and none received antifungal therapy. On visiting the patients at their homes, two were reported to have died of unknown causes. The third patient was found alive and well and had experienced local spontaneous healing.

CONCLUSION

Basidiobolomycosis is a rare subcutaneous fungal disease mimicking preulcerative Buruli ulcer. We stress the importance of the early recognition by clinicians and pathologists of this treatable disease, so patients can timely receive antifungal therapy.

The first entomophthoralean killing millipedes, Arthrophaga myriapodina n. gen. n. sp., causes climbing before host death

A new species and genus of entomophthoralean fungus, Arthrophaga myriapodina kills polydesmid millipedes. This species was first seen over a century ago but never described. It is the first millipede pathogen known from the order Entomophthorales, species of which are best known as pathogens of a wide diversity of insects. The fungus induces pre-death climbing behavior in its hosts, enabling the fungus to broadcast its forcibly-discharged conidia from a high vantage, which presumably increases the fitness of the fungus. Study of herbarium specimens and photographic discoveries on the internet suggest the fungus occurs widely in eastern North America.

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences

The usage of molecular phylogenetic approaches is critical to advance the understanding of systematics and community processes in the kingdom Fungi. Among the possible phylogenetic markers (or combinations of them), the 18S rRNA gene appears currently as the most prominent candidate due to its large availability in public databases and informative content. The purpose of this work was the creation of a reference phylogenetic framework that can serve as ready-to-use package for its application on fungal classification and community analysis. The current database contains 9329 representative 18S rRNA gene sequences covering the whole fungal kingdom, a manually curated alignment, an annotated and revised phylogenetic tree with all the sequence entries, updated information on current taxonomy, and recommendations of use. Out of 201 total fungal taxa with more than two sequences in the dataset, 179 were monophyletic. From another perspective, 66% of the entries had a tree-derived classification identical to that obtained from the NCBI taxonomy, whereas 34% differed in one or the other rank. Most of the differences were associated to missing taxonomic assignments in NCBI taxonomy, or the unexpected position of sequences that positioned out of their theoretically corresponding clades. The strong correlation observed with current fungal taxonomy evidences that 18S rRNA gene sequence-based phylogenies are adequate to reflect genealogy of Fungi at the levels of order and above, and justify their further usage and exploration.

Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

Obligate parasites are under strong selection to increase exploitation of their host to survive while evading detection by host immune defences. This has often led to elaborate pathogen adaptations and extreme host specificity. Specialization on one host, however, often incurs a trade-off influencing the capacity to infect alternate hosts. Here, we investigate host adaptation in two morphologically indistinguishable and closely related obligate specialist insect-pathogenic fungi from the phylum Entomophthoromycota, Entomophthora muscae sensu stricto and E. muscae sensu lato, pathogens of houseflies (Musca domestica) and cabbage flies (Delia radicum), respectively. We compared single nucleotide polymorphisms within and between these two E. muscae species using 12 RNA-seq transcriptomes from five biological samples. All five isolates contained intra-isolate polymorphisms that segregate in 50:50 ratios, indicative of genetic duplication events or functional diploidy. Comparative analysis of dN/dS ratios between the multinucleate E. muscae s.str. and E. muscae s.l. revealed molecular signatures of positive selection in transcripts related to utilization of host lipids and the potential secretion of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar utilization was probably important for the evolutionary transition to obligate insect pathogenicity in E. muscae. These results support the hypothesis that genetically based host specialization in specialist pathogens evolves in response to the challenge of using resources and dealing with the immune system of different hosts.