21 results found
Henk DA, Shahar-Golan R, Devi KR, et al., 2012, Clonality Despite Sex: The Evolution of Host-Associated Sexual Neighborhoods in the Pathogenic Fungus Penicillium marneffei, PLOS PATHOGENS, Vol: 8, ISSN: 1553-7366
Voelz K, Johnston SA, Farrer RA, et al., 2012, Diverse genetic adaptation to host-specific stresses mediates hypervirulence in Cryptococcus gattii, MYCOSES, Vol: 55, Pages: 64-64, ISSN: 0933-7407
Fisher MC, Henk DA, 2012, Sex, drugs and recombination: the wild life of Aspergillus, Vol: 21, Pages: 1305-1306, ISSN: 1365-294X
Throughout the eukaryotes, sexual reproduction is an almost universal phenomenon. However, within the Kingdom Fungi, this relationship is not so clear-cut. Fungi exhibit a spectrum of reproductive modes and life-cycles; amongst the better known species, sexual reproduction is often facultative, can be rare, and in over half of the known Ascomycota (the moulds) is unknown (Taylor et al. 1999). However, over the last decade, it has become apparent that many of these asexual mitosporic taxa undergo cryptic recombination via unobserved mechanisms and that wholly asexual fungi are, in fact, a rarity (Taylor et al. 1999, 2001; Heitman 2010). This revolution in our understanding of fungal sexuality has come about in two ways: Firstly, sexual reproduction leaves an imprint on fungal genomes by maintaining genes required for mating and by generating patterns of mutation and recombination restricted to meiotic processes. Secondly, scientists have become better at catching fungi in flagrante delicto. The genus Aspergillus is one such fungus where a combination of population genetics, genomics and taxonomy has been able to intuit the existence of sex, then to catch the fungus in the act and formally describe their sexual stages. So, why are sexy moulds exciting? One species in particular, Aspergillus flavus, is notorious for its ability to produce a diverse array of secondary metabolites, of which the polyketide aflatoxins (AF) are carcinogenic and others (such as cyclopiazonic acid) are toxigenic. Because of the predilection of A. flavus to grow on crops, such as peanuts, corn and cotton, biocontrol is widely used to mitigate infection by pre-applying nonaflatoxigenic (AF-) strains to competitively exclude the wild-type AF+ strains. However, the eventual fate in nature of these biocontrol strains is not known. In this issue of Molecular Ecology, Olarte et al. (2012) make an important contribution by using laboratory crosses of A. flavus to show that not only is AF highly herit
Fisher MC, Henk DA, Briggs C, et al., 2012, Emerging fungal threats to animal, plant and ecosystem health., Nature, Pages: 186-194
Henk DA, Fisher MC, 2012, The gut fungus Basidiobolus ranarum has a large genome and different copy numbers of putatively functionally redundant elongation factor genes, Vol: 7, ISSN: 1932-6203
Fungal genomes range in size from 2.3 Mb for the microsporidian Encephalitozoon intestinalis up to 8000 Mb for Entomophaga aulicae, with a mean genome size of 37 Mb. Basidiobolus, a common inhabitant of vertebrate guts, is distantly related to all other fungi, and is unique in possessing both EF-1alpha and EFL genes. Using DNA sequencing and a quantitative PCR approach, we estimated a haploid genome size for Basidiobolus at 350 Mb. However, based on allelic variation, the nuclear genome is at least diploid, leading us to believe that the final genome size is at least 700 Mb. We also found that EFL was in three times the copy number of its putatively functionally overlapping paralog EF-1alpha. This suggests that gene or genome duplication may be an important feature of B. ranarum evolution, and also suggests that B. ranarum may have mechanisms in place that favor the preservation of functionally overlapping genes.
Henk DA, Fisher MC, 2011, Genetic Diversity, Recombination, and Divergence in Animal Associated Penicillium dipodomyis, PLOS ONE, Vol: 6, ISSN: 1932-6203
Henk DA, Farr DF, Aime MC, 2011, Mycodiplosis (Diptera) infestation of rust fungi is frequent, wide spread and possibly host specific, Fungal Ecol, Vol: 4, Pages: 284-289, ISSN: 1754-5048
Insect mycophagy is considered common but generally lacking host-specificity. Larvae of some Mycodiplosis species (Insecta, Diptera) feed primarily on spores of rust fungi (Basidiomycota, Pucciniales). The number of rust-feeding species and their relative frequency, distribution, and degree of host-specificity are not known. A survey of 200 recent rust collections from around the world, and a systematic survey of 333 herbarium specimens from Maryland show that Mycodiplosis infestation is very common. Desiccated larvae were found on specimens dating back as far as 1886, the oldest collection in the survey. Greater than 20 % of all rust collections examined were infested with Mycodiplosis larvae. In Maryland infestation frequencies were similar at different spatial scales, but different rust species varied in their frequency of infestation. Primers were designed to target Mycodiplosis 28S rDNA, and sequence data revealed genetic variation between Mycodiplosis isolates from different rust species. (C) 2011 Elsevier Ltd and The British Mycological Society. All rights reserved.
Henk DA, Eagle CE, Brown K, et al., 2011, Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus, Mol Ecol, Vol: 20, Pages: 4288-4301, ISSN: 0962-1083
Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only slight differences detected in physiology. We found each species in air and dust samples collected in and around St Mary's Hospital where Fleming worked. Genotyping of 30 markers across the genome showed that preserved fungal material from Fleming's laboratory was nearly identical to derived strains currently in culture collections and in the same distinct species as a wild progenitor strain of current penicillin producing industrial strains rather than the type species P. chrysogenum. Global samples of the two most common species were found to possess mating-type genes in a near 1:1 ratio, and show evidence of recombination with little geographic population subdivision evident. However, no hybridization was detected between the species despite an estimated time of divergence of less than 1 MYA. Growth studies showed significant interspecific inhibition by P. chrysogenum of the other common species, suggesting that competition may facilitate species maintenance despite globally overlapping distributions. Results highlight under-recognized diversity even among the best-known fungal groups and the potential for speciation despite overlapping distribution.
Meece JK, Anderson JL, Fisher MC, et al., 2011, Population Genetic Structure of Clinical and Environmental Isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers, Appl Environ Microb, Vol: 77, Pages: 5123-5131, ISSN: 0099-2240
Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and alpha-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.
Simwami SP, Khayhan K, Henk DA, et al., 2011, Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin, Plos Pathog, Vol: 7, ISSN: 1553-7366
The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year, causing up to a third of all AIDS-related deaths. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly-virulent emerging lineages are changing patterns of human disease both temporally and spatially. Cryptococcus neoformans variety grubii (Cng, serotype A) constitutes the most ubiquitous cause of cryptococcal meningitis worldwide, however patterns of molecular diversity are understudied across some regions experiencing significant burdens of disease. We compared 183 clinical and environmental isolates of Cng from one such region, Thailand, Southeast Asia, against a global MLST database of 77 Cng isolates. Population genetic analyses showed that Thailand isolates from 11 provinces were highly homogenous, consisting of the same genetic background (globally known as VNI) and exhibiting only ten nearly identical sequence types (STs), with three (STs 44, 45 and 46) dominating our sample. This population contains significantly less diversity when compared against the global population of Cng, specifically Africa. Genetic diversity in Cng was significantly subdivided at the continental level with nearly half (47%) of the global STs unique to a genetically diverse and recombining population in Botswana. These patterns of diversity, when combined with evidence from haplotypic networks and coalescent analyses of global populations, are highly suggestive of an expansion of the Cng VNI clade out of Africa, leading to a limited number of genotypes founding the Asian populations. Divergence time testing estimates the time to the most common ancestor between the African and Asian populations to be 6,920 years ago (95% HPD 122.96 - 27,177.76
Liang L, Cao CW, Wang WJ, et al., 2011, Common Reservoirs for Penicillium marneffei Infection in Humans and Rodents, China, Emerg Infect Dis, Vol: 17, Pages: 209-214, ISSN: 1080-6040
Human penicilliosis marneffei is an emerging infectious disease caused by the fungus Penicillium marneffei. High prevalence of infection among bamboo rats of the genera Rhizomys and Cannomys suggest that these rodents are a key facet of the P marneffei life cycle. We trapped bamboo rats during June 2004-July 2005 across Guangxi Province, China, and demonstrated 100% prevalence of infection. Multi locus genotypes show that P marneffei isolates from humans are similar to those infecting rats and are in some cases identical. Comparison of our dataset with genotypes recovered from sites across Southeast Asia shows that the overriding component of genetic structure in P marneffei is spatial, with humans containing a greater diversity of genotypes than rodents. Humans and bamboo rats are sampling an as-yet undiscovered common reservoir of infection, or bamboo rats are a vector for human infections by acting as amplifiers of infectious dispersal stages.
Farrer RA, Weinert LA, Bielby J, et al., 2011, Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage, Vol: 108
Walker SF, Bosch J, Gomez V, et al., 2010, Factors driving pathogenicity vs. prevalence of amphibian panzootic chytridiomycosis in Iberia, Ecol Lett, Vol: 13, Pages: 372-382, ISSN: 1461-023X
P>Amphibian chytridiomycosis is a disease caused by the fungus Batrachochytrium dendrobatidis (Bd). Whether Bd is a new emerging pathogen (the novel pathogen hypothesis; NPH) or whether environmental changes are exacerbating the host-pathogen dynamic (the endemic pathogen hypothesis; EPH) is debated. To disentangle these hypotheses we map the distribution of Bd and chytridiomycosis across the Iberian Peninsula centred on the first European outbreak site. We find that the infection-free state is the norm across both sample sites and individuals. To analyse this dataset, we use Bayesian zero-inflated binomial models to test whether environmental variables can account for heterogeneity in both the presence and prevalence of Bd, and heterogeneity in the occurrence of the disease, chytridiomycosis. We also search for signatures of Bd-spread within Iberia using genotyping. We show (1) no evidence for any relationship between the presence of Bd and environmental variables, (2) a weak relationship between environmental variables and the conditional prevalence of infection, (3) stage-dependent heterogeneity in the infection risk, (4) a strong association between altitude and chytridiomycosis, (5) multiple Iberian genotypes and (6) recent introduction and spread of a single genotype of Bd in the Pyrenees. We conclude that the NPH is consistent with the emergence of Bd in Iberia. However, epizootic forcing of infection is tied to location and shaped by both biotic and abiotic variables. Therefore, the population-level consequences of disease introduction are explained by EPH-like processes. This study demonstrates the power of combining surveillance and molecular data to ascertain the drivers of new emerging infections diseases.
Arnold AE, Henk DA, Eells RL, et al., 2007, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR, Mycologia, Vol: 99, Pages: 185-206, ISSN: 0027-5514
We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, USA, with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 by of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility. but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultu
Henk DA, Vilgalys R, 2007, Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium, Am J Bot, Vol: 94, Pages: 1515-1526, ISSN: 0002-9122
In the Pucciniomycetes, a class of fungi that includes the plant pathogenic rust fungi, insect parasitism is restricted to a single family, the Septobasidiaceae. The Septobasidiaceae form a variety of symbioses with scale insects and have remained largely unstudied since the 1930s. Transitions between plant and animal parasitism and between mutualism and parasitism cannot be fully addressed in the Basidiomycota without a clear phylogenetic hypothesis for the Septobasidiales. Here, molecular phylogenetic methods were applied to understand the origin of scale insect parasitism, test the monophyly of the order Septobasidiales, and evaluate the infrageneric concepts in the largest genus of scale insect parasites, Septobasidium. DNA sequence data from rRNA genes were used to infer higher-level relationships within the Pucciniomycetes, and data from translation elongation factor 1-alpha (tefl) were added for phylogenetic inference within the Septobasidiaceae. Data from tefl revealed different intron arrangements within Septobasidium, but the molecule did not provide much additional phylogenetically informative data. Likelihood-model-based phylogenetic analyses of 44 Pucciniomycotina taxa provided moderate support for a single origin of insect parasitism. Within the Septobasidiaceae, there was little or no support for a monophyletic Septobasidium, and well-resolved subclades of Septobasidium species contradict previous morphological delimitations of groups within the genus.
Henk DA, 2006, Coevolutionary diversification in Septobasidium, a fungal symbiont of scale insects
Aime MC, Matheny PB, Henk DA, et al., 2006, An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences, Mycologia, Vol: 98, Pages: 896-905, ISSN: 0027-5514
In this study we provide a phylogenetically based introduction to the classes and orders of Pucciniomycotina (=Urediniomycetes), one of three subphyla of Basidiomycota. More than 8000 species of Pucciniomycotina have been described including putative saprotrophs and parasites of plants, animals and fungi. The overwhelming majority of these (similar to 90%) belong to a single order of obligate plant pathogens, the Pucciniales (=Uredinales), or rust fungi. We have assembled a dataset of previously published and newly generated sequence data from two nuclear rDNA genes (large subunit and small subunit) including exemplars from all known major groups in order to test hypotheses about evolutionary relationships among the Pucciniomycotina. The utility of combining nuc-lsu sequences spanning the entire D1-D3 region with complete nuc-ssu sequences for resolution and support of nodes is discussed. Our study confirms Pucciniomycotina as a monophyletic group of Basidiomycota. In total our results support eight major clades ranked as classes (Agaricostilbomycetes, Atractiellomycetes, Classiculomycetes, Cryptomycocolacomycetes, Cystobasidiomycetes, Microbotryomycetes, Mixiomycetes and Pucciniomycetes) and 18 orders.
Henk DA, 2005, New species of Septobasidium from southern Costa Rica and the southeastern United States, Mycologia, Vol: 97, Pages: 908-913, ISSN: 0027-5514
New species are described in Septobasidium, a genus of urediniomycete parasites on scale insects. One new species, S. gomezii, is described from Costa Rica, and another, S. meredithiae, is described from Louisiana. S. gomezii is most similar to S. septobasidioides, but macroscopic and microscopic differences support it being a distinct species. S. meredithiae is similar to S. alni and S. castaneum but differs from these species in several macroscopic and microscopic characters, especially when the species are observed on the same host tree and insect species. Another species collected only once in Costa Rica is listed with observations but it is not formally described here. This Septobasidium species shares some key characteristics with S. ramorum but combines a dense, compact, nearly black thallus and pigmented probasidia-like structures with spindle-shaped haustoria. Implications for taxonomy, morphological evolution and host specificity in Septobasidium are discussed.
Gomez LD, Henk DA, 2004, Validation of the species of Septobasidium described by John N. Couch, Vol: 4
Henk DA, Weir A, Blackwell M, 2003, Laboulbeniopsis termitarius, an ectoparasite of termites newly recognized as a member of the Laboulbeniomycetes, Mycologia, Vol: 95, Pages: 561-564, ISSN: 0027-5514
Minute fungi associated with termites have caused taxonomic problems in the past due to their autapomorphic and highly reduced morphologies. DNA sequence data from one such enigmatic fungus, Laboulbeniopsis termitarius, supports its phylogenctic position as member of a laboulbeniomycete clade within the Ascomycota. This clade is composed entirely of fungi associated with arthropods, often as parasites, and the inclusion of L. termitarius supports the single origin of thallus development by means of enlargement and division of the spore.
Blackwell M, Henk DA, Jones KG, 2003, Extreme morphological divergence: phylogenetic position of a termite ectoparasite, Mycologia, Vol: 95, Pages: 987-992, ISSN: 0027-5514
Species of Termitaria are lesion-forming ectoparasites occurring worldwide on a diverse group of termites. The reduced thallus consists of a basal cell layer from which haustorial cells penetrate the termite and a darkly pigmented sporodochium. One species, Termitaria snyderi, has been the subject of several morphological studies, but its phylogenetic position has remained enigmatic. Here we provide evidence of a close relationship between T. snyderi and the morphologically distinct ascomycetes, Kathistes analemmoides and K. calyculata, based on phylogenetic analysis of molecular characters derived from portions of the nuclear-encoded small-subunit ribosomal RNA gene (ssu rDNA) and supplemental evidence from the beta-tubulin gene. Trees were derived using parsimony and maximum-likelihood criteria. Bayesian analysis and parsimony bootstrap methods were used to assess support for the tree nodes.
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.