Kerry O'Donnell

Molecular systematics and phylogeography of the Gibberella fujikuroi species complex.

Phylogenetic relationships of the phyto-pathogenic Gibberella fujikuroi species complex were investigated by maximum parsimony analysis of DNA sequences from multiple loci. Gene trees inferred from...

FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium

One of the greatest impediments to the study of Fusarium has been the incorrect and confused application of species names to toxigenic and pathogenic isolates, owing in large part to intrinsic limitations of morphological species recognition and its application. To address this problem, we have created FUSARIUM-ID v. 1.0, a publicly available database of partial translation elongation factor 1-alpha (TEF) DNA sequences, presently representing a selected sample of the diversity of the genus diversity, with excellent representation of Type-B trichothecene toxin producers, and the Gibberella fujikuroi, Fusarium oxysporum and F. solani species complexes. Users can generate sequences using primers that are conserved across the genus, and use the sequence as a query to BLAST the database, which can be accessed at http://fusarium.cbio.psu.edu, or in a phylogenetic analysis. Correct identification of a known species in these groups often can be performed using this gene region alone. This growing database will contain only vouchered sequences attached to publicly available cultures. In the future, FUSARIUM-ID will be expanded to include additional sequences, including multiple sequences from the same species, sequences from new and revised species, and information from additional genes.

The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium

Filamentous fungi within the Fusarium graminearum species complex (Fg complex) are the primary etiological agents of Fusarium head blight (scab) of wheat and barley. Scab is an economically devastating plant disease that greatly limits grain yield and quality. In addition, scabby grain is often contaminated with trichothecene mycotoxins that act as virulence factors on some hosts, and pose a serious threat to animal health and food safety. Strain-specific differences in trichothecene metabolite profiles (chemotypes) are not well correlated with the Fg complex phylogeny based on genealogical concordance at six single-copy nuclear genes. To examine the basis for this discord between species and toxin evolution, a 19-kb region of the trichothecene gene cluster was sequenced in 39 strains chosen to represent the global genetic diversity of species in the Fg complex and four related species of Fusarium. Phylogenetic analyses demonstrated that polymorphism within these virulence-associated genes is transspecific and appears to have been maintained by balancing selection acting on chemotype differences that originated in the ancestor of this important group of plant pathogens. Chemotype-specific differences in selective constraint and evidence of adaptive evolution within trichothecene genes are also reported.

New Fusarium species and combinations within the Gibberella fujikuroi species complex

Ten Fusarium species within the Gibberella fujikuroi complex are described and illustrated as new species: F. acutatum ex Triticum sp. (wheat) and Cajanus sp.,F. begoniae ex Begonia elatior hybrid,...

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomycete Fusarium sambucinum (Gibberella pulicaris)

SummaryVariation within the internal transcribed spacers (ITS1 and ITS2) and 5.8s ribosomal DNA gene of the heterothallic phytopathogenic filamentous fungus, Fusarium sambucinum (teleomorph=Gibberella pulicaris), was examined in 86 strains from diverse geographical locations by PCR amplification and direct sequencing in order to measure intraspecific divergence within the ITS region. Sequence analysis revealed three ITS types (A, B, C), within which divergence was extremely low (0–2.3%). Surprisingly, the level of intraspecific divergence observed between ITS types, A→B=14.3%, A→C=15%, and B→C=4.6%, is much greater than that reported for any other species. The degree to which transition/transversions and insertion/deletions make up the pattern of ITS sequence evolution both within and between types was analyzed. The sequences of the ITS types exhibit a C-T transition bias together with a GC insertion/deletion bias. In comparison, the genic flanking sequences, including the 5.8s rDNA gene and 5′ end of the 28s large nuclear rDNA, are highly conserved. By the criteria of mating and DNA-DNA hybridization, all the strains examined represent a single species. Discordance between the ITS sequence data and other molecular and genetic data on F. sambucinum is discussed.

Gene genealogies and AFLP analyses in the Fusarium oxysporum complex identify monophyletic and nonmonophyletic formae speciales causing wilt and rot disease

ABSTRACT The monophyletic origin of host-specific taxa in the plant-pathogenic Fusarium oxysporum complex was tested by constructing nuclear and mitochondrial gene genealogies and amplified fragment length polymorphism (AFLP)-based phylogenies for 89 strains representing the known genetic and pathogenic diversity in 8 formae speciales associated with wilt diseases and root and bulb rot. We included strains from clonal lineages of F. oxysporum f. spp. asparagi, dianthi, gladioli, lilii, lini, opuntiarum, spinaciae, and tulipae. Putatively nonpathogenic strains from carnation and lily were included and a reference strain from each of the three main clades identified previously in the F. oxysporum complex; sequences from related species were used as outgroups. DNA sequences from the nuclear translation elongation factor 1alpha and the mitochondrial small subunit (mtSSU) ribosomal RNA genes were combined for phylogenetic analysis. Strains in vegetative compatibility groups (VCGs) shared identical sequences and AFLP profiles, supporting the monophyly of the two single-VCG formae speciales, lilii and tulipae. Identical genotypes were also found for the three VCGs in F. oxysporum f. sp. spinaciae. In contrast, multiple evolutionary origins were apparent for F. oxysporum f. spp. asparagi, dianthi, gladioli, lini, and opuntiarum, although different VCGs within each of these formae speciales often clustered close together or shared identical EF-1alpha and mtSSU rDNA haplotypes. Kishino-Hasegawa analyses of constraints forcing the monophyly of these formae speciales supported the exclusive origin of F. oxysporum f. sp. opuntiarum but not the monophyly of F. oxysporum f. spp. asparagi, dianthi, gladioli, and lini. Most of the putatively nonpathogenic strains from carnation and lily, representing unique VCGs, were unrelated to F. oxysporum f. spp. dianthi and lilii, respectively. Putatively nonpathogenic or rot-inducing strains did not form exclusive groups within the molecular phylogeny. Parsimony analyses of AFLP fingerprint data supported the gene genealogy-based phylogram; however, AFLP-based phylogenies were considerably more homoplasious than the gene genealogies. The predictive value of the forma specialis naming system within the F. oxysporum complex is questioned.

Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment.

ABSTRACT Members of the Fusarium solani species complex (FSSC) are increasingly implicated as the causative agents of human mycoses, particularly in the expanding immunocompromised and immunosuppressed patient populations. Best known as ubiquitous plant pathogens and saprotrophs, the FSSC comprises over 45 phylogenetically distinct species distributed among three major clades. To identify which species are associated with human infections, we generated multilocus haplotypes based on four partial gene sequences from 471 isolates. Of these, 278 were from human patients, 21 were from hospital environments, and 172 were from other sources. Phylogenetic trees inferred from an ergosterol biosynthesis gene (erg-3) were highly discordant with those inferred from the three other partial gene sequences; therefore, this partition was analyzed separately. Multilocus analysis showed that isolates from humans were restricted to but spread throughout clade 3 of the FSSC phylogeny, comprising at least 18 phylogenetically distinct species. The majority (74.5%) of the clinical isolates, however, were associated with four major lineages, designated groups 1 to 4. Groups 1 and 2 were strongly supported as phylogenetic species, whereas groups 3 and 4 were not. Although isolates from ocular infections were found in all four groups, they had a significant tendency to belong to group 3 (P < 0.001). Human clinical isolates shared identical multilocus haplotypes with isolates from plants, other animals, and from hospital environments, suggesting potential nosocomiality. The major finding of this study is that FSSC-associated mycoses of humans and other animals have origins in a broad phylogenetic spectrum, indicating widespread ability to cause infection in this diverse species complex.

Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis

Phylogenetic relationships among asco- mycetous truffles and the true and false morels were examined by using sequences from two nuclear en- coded ribosomal DNA genes. The data consist of 18S rDNA and partial 28S rDNA sequences for 29 taxa. Individual and combined data sets were analyzed by maximum parsimony (MP), neighbor-joining (NJ) and maximum likelihood (ML) methods. Parsimony analysis of the combined data set, which contained 3 published 18S sequences and consisted of 2358 nu- cleotide characters, yielded a single most parsimoni- ous tree of 1728 steps. The results indicate that the hypogeous ascomycetous truffle and trufflelike taxa studied represent at least 5 independent lineages within the Pezizales. Results also suggest that several epigeous and most hypogeous taxa have been mis- placed taxonomically. Bootstrap analyses show strong support for a Tuberaceae-Helvellaceae clade which is a monophyletic sister group of a Morchellaceae-Dis- cinaceae clade. Rhizina is a sister group to both of these clades in the MP and ML trees while in the NJ tree it is a sister of the Morchellaceae-Discinaceae clade. MP, ML, and NJ tree topologies indicate that Rhizina should be removed from the Helvellaceae and classified in a monotypic family, the Rhizinaceae. A phylogenetically-based classification for these fungi is proposed together with emendations of 4 families.