Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab

Four or more species of Cladosporium sympatrically colonize Phragmites australis

A collection of Cladosporium has been recovered from common reed growing at Lake Constance (Germany). High-resolution cryo-scanning electron microscopy revealed that Cladosporium isolates from reed are diverse. Morphologically, we distinguished three species, viz. C. herbarum, C. oxysporum, and Cladosporium sp. Internal transcribed spacer (ITS) sequence analysis supported these results and, moreover, separated the most common species, C. oxysporum, into two subclades. Two additional phylogenies were generated to gain support for this finding. The first, differentiating fungi by their capacities to metabolize different carbon sources, showed correlation with morphology. The second, based on actin gene sequences, showed the same overall topology as that of the ITS tree, but resulted in a higher resolution indicating the existence of four or more species of Cladosporium on reed. A nested PCR assay targeting variable sequences within actin introns indicated that these four species sympatrically colonize reed. There was no evidence for mutual exclusion on or within the host or specialization for host habitats or organs.

The internet-based fungal pathogen database: a proposed model

ABSTRACT A better understanding of the phenotypic and genetic diversity of significant agricultural pathogens and how their populations change in the field is critical for designing successful, long-term disease management strategies. Although efforts to determine the genetic diversity of plant pathogens have substantially increased in recent years, mainly due to the availability of various molecular tools, complementary efforts to archive and integrate the resulting data have been very limited. As a consequence, it is often difficult to compare the available data from various laboratories because the data have been generated by diverse tools, often preventing any direct comparisons, and are saved in a format that is unsuitable for comparative studies. The establishment of an internet-based database that cross-links the digitized genotypic and phenotypic information of individual pathogens at both the species and population levels may allow us to effectively address these problems by coordinating the generation of data and its subsequent archiving. We discuss the needs, benefits, and potential structure of such a database.

Evolution of Fusarium oxysporum f. sp. vasinfectum Races Inferred from Multigene Genealogies

ABSTRACT Fusarium wilt of cotton is a serious fungal disease responsible for significant yield losses throughout the world. Evolution of the causal organism Fusarium oxysporum f. sp. vasinfectum, including the eight races described for this specialized form, was studied using multigene genealogies. Partial sequences of translation elongation factor (EF-1alpha), nitrate reductase (NIR), phosphate permase (PHO), and the mitochondrial small subunit (mtSSU) rDNA were sequenced in 28 isolates of F. oxysporum f. sp. vasinfectum selected to represent the global genetic diversity of this forma specialis. Results of a Wilcoxon Signed-Ranks Templeton test indicated that sequences of the four genes could be combined. In addition, using combined data from EF-1alpha and mtSSU rDNA, the phylogenetic origin of F. oxysporum f. sp. vasinfectum within the F. oxysporum complex was evaluated by the Kishino-Hasegawa likelihood test. Results of this test indicated the eight races of F. oxysporum f. sp. vasinfectum appeared to be nonmonophyletic, having at least two independent, or polyphyletic, evolutionary origins. Races 3 and 5 formed a strongly supported clade separate from the other six races. The combined EF-1alpha, NIR, PHO, and mtSSU rDNA sequence data from the 28 isolates of F. oxysporum f. sp. vasinfectum recovered four lineages that correlated with differences in virulence and geographic origin: lineage I contained race 3, mostly from Egypt, and race 5 from Sudan; lineage II contained races 1, 2, and 6 from North and South America and Africa; lineage III contained race 8 from China; and lineage IV contained isolates of races 4 and 7 from India and China, respectively.

Molecular Relationships of Fungi Within the Fusarium redolens-F. hostae Clade

ABSTRACT The evolutionary relationships of fungi in the Fusarium redolens-F. hostae clade were investigated by constructing nuclear and mitochondrial gene genealogies for 37 isolates representing the known genetic and pathogenic diversity of this lineage, together with 15 isolates from putative sister groups that include the Gibberella fujikuroi and F. oxysporum species complexes and related species. Included in the analyses were 29 isolates of F. redolens from Asparagus, Convallaria, Dianthus, Fritillaria, Hebe, Helleborus, Hordeum, Linum, Pisum, Pseudotsuga, and Zea spp., and from soil. Isolates of F. hostae analyzed included two reference isolates from Hosta spp. and six isolates from Hyacinthus spp. that originally were classified as F. oxysporum f. sp. hyacinthi. DNA sequences from a portion of the nuclear translation elongation factor 1alpha (EF-1alpha) gene and the mitochondrial small subunit (mtSSU) ribosomal RNA (rRNA) were analyzed individually and as a combined data set based on results of the nonparametric Wilcoxon signed ranks Templeton combinability test. Maximum parsimony analysis of the combined data set identified the F. redolens-F. hostae clade as a sister group to a phylogenetically diverse clade in which the G. fujikuroi species complex formed the most basal lineage. Also included in this latter clade were two unnamed Fusarium spp. that are morphologically similar to F. oxysporum and putative sister taxa comprising the F. oxysporum complex and a F. nisikadoi-F. miscanthi clade. Phylogenetic diversity in F. redolens was small; all isolates were represented by only three EF-1alpha and two mtSSU rDNA haplotypes. Both the isolates of F. redolens f. sp. asparagi and those of F. redolens f. sp. dianthi were nearly evenly distributed in the combined molecular phylogeny between the two major subclades within F. redolens.

Fast methods for screening of trichothecenes in fungal cultures using gas chromatography-tandem mass spectrometry

The paper presents a fast method for trichothecene profiling and chemotaxonomic studies in species of Fusarium, Stachybotrys. Trichoderma and Memnoniella. Micro scale extracted crude Fusarium extracts were derivatised using pentafluoropropionic anhydride and analysed by gas chromatography with simultaneous full scan and tandem mass spectrometric detection. It was possible to monitor for up to four compounds simultaneous, making detection of acetyl T-2 toxin, T-2 toxin, HT-2 toxin, T-2 triol. T-2 tetraol, neosolaniol, iso-neosolaniol, scirpentriol, 4,15-diacetoxyscirpenol, 15-acetoxyscirpenol, 4-acetoxyscirpentriol, nivalenol, fusarenon-X, deoxynivalenol, 15-acetyl-deoxynivalenol and 3-acetyldeoxynivalenol possible during a 23-min GC run. A slightly modified method could detect trichothecenes produced by Stachybotrys, Memnoniella and Trichoderma, by hydrolysing crude extracts prior to derivatisation with heptafluorobuturyl imidazole. All types of derivatised extracts could be reanalysed using negative ion chemical ionisation (NICI) GC-MS for molecular mass determination and verification purposes. A retention time index could be used for correction in retention time drifts between sequences and worked both in EI+ and NICI mode.

Microbial toxins in plant-pathogen interactions: Biosynthesis, resistance mechanisms, and significance

In the history of phytopathology, microbial toxins have been the objects of extensive studies as possible pathogenicity or virulence factors for the producer pathogens. The recent development of molecular genetic techniques provided an experimental basis to thoroughly test the role of these secondary metabolites in pathogenesis. Some of them did prove to be highly associated with disease initiation or enhanced virulence in certain plant-pathogen interactions. In this review, we describe recent progresses in the field of plant-pathogen interactions focusing on two toxins; i.e., tabtoxin from Pseudomonas syringae and trichothecenes from Fusarium and other fungi. These microbial toxins have convincingly been shown to play causal roles in plant disease development. Studies on the biosynthesis and resistance mechanisms of these producers are outlined, and the significance of this knowledge is discussed in relation to practical applications in agriculture.

Species concepts in the Cylindrocladium floridanum and Cy. spathiphylli complexes (Hypocreaceae) based on multi-allelic sequence data, sexual compatibility and morphology

Much attention has recently been devoted to the delimitation of species units in Cylindrocladium (Cy.). In this regard the present study focuses on the taxa within the unresolved Cy. floridanum and Cy. spathiphylli species complexes. Maximum parsimony analyses of DNA sequences of ITS, beta-tubulin and histone regions of rRNA genes, and mating experiments revealed a geographically isolated species of Cylindrocladium in the Cy. spathiphylli (teleomorph: Calonectria spathiphylli) species complex. Cy. pseudospathiphylli sp. nov. (teleomorph: Ca. pseudospathiphylli sp. nov.) is described as a new phylogenetic, biological and morphological species. It is distinguished from Cy. spathiphylli by being homothallic, having smaller macroconidia, and distinct DNA sequences of beta-tubulin and histone genes. Similarly, parsimony analysis of a combined data set also indicated several phylogenetic species to exist within Cy. floridanum (teleomorph: Ca. kyotensis). Based on differences in vesicle morphology and conidium dimensions, the Canadian population of Cy. floridanum, formerly known as Cy. floridanum Group 2, is described as Cy. canadense sp. nov., while a further collection from Hawaii is described as Cy. pacificum sp. nov.

Gene genealogies, cryptic species, and molecular evolution in the human pathogen Coccidioides immitis and relatives (Ascomycota, Onygenales)

Previous genealogical analyses of population structure in Coccidioides immitis revealed the presence of two cryptic and sexual species in this pathogenic fungus but did not clarify their origin and relationships with respect to other taxa. By combining the C. immitis data with those of two of its closest relatives, the free-living saprophytes Auxarthron zuffianum and Uncinocarpus reesii, we show that the C. immitis species complex is monophyletic, indicating a single origin of pathogenicity. Cryptic species also were found in both A. zuffianum and U. reesii, indicating that they can be found in both pathogenic and free-living fungi. Our study, together with a few others, indicates that the current list of known fungal species might be augmented by a factor of at least two. However, at least in the C. immitis, A. zuffianum, and U. reesii complexes, cryptic species represent subdivisions at the tips of deep monophyletic clades and thus well within the existing framework of generic classification. An analysis of silent and expressed divergence and polymorphism values between and within the taxa identified by genealogical concordance did not reveal faster evolution in C. immitis as a consequence of adaptation to the pathogenic habit, nor did it show positive Darwinian evolution in a region of a dioxygenase gene (tcrP gene coding for 4-HPPD) known to cause antigenic responses in humans. Instead, the data suggested relative stasis, indicative of purifying selection against mostly deleterious mutations. Two introns in the same gene fragment were considerably more divergent than exons and were unalignable between species complexes but had very low polymorphism within taxa.

Identification of deoxynivalenol- and nivalenol-producing chemotypes of Gibberella zeae by using PCR

Gibberella zeae, a major cause of cereal scab, may be divided into two chemotypes based on production of the trichothecenes deoxynivalenol (DON) and nivalenol (NIV). We cloned and sequenced the gene cluster for trichothecene biosynthesis from each chemotype. G. zeae H-11 is a DON producer isolated from corn, and G. zeae 88-1 is a NIV producer from barley. We sequenced a 23-kb gene cluster from H-11 and a 26-kb cluster from 88-1, along with the unlinked Tri101 genes. Each gene cluster contained 10 Tri gene homologues in the same order and transcriptional directions as those of Fusarium sporotrichioides. Between H-11 and 88-1 all of the Tri homologues except Tri7 were conserved, with identities ranging from 88 to 98% and 82 to 99% at the nucleotide and amino acid levels, respectively. The Tri7 sequences were only 80% identical at the nucleotide level. We aligned the Tri7 genes and found that the Tri7 open reading frame of H-11 carried several mutations and an insertion containing 10 copies of an 11-bp tandem repeat. The Tri7 gene from 88-1 carried neither the repeat nor the mutations. We assayed 100 G. zeae isolates of both chemotypes by PCR amplification with a primer pair derived from the Tri7 gene and could differentiate the chemotypes by polyacrylamide gel electrophoresis. The PCR-based method developed in this study should provide a simple and reliable diagnostic tool for differentiating the two chemotypes of G. zeae.

A Genetic and Biochemical Approach to Study Trichothecene Diversity in Fusarium sporotrichioides and Fusarium graminearum

The trichothecenes T-2 toxin and deoxynivalenol (DON) are natural fungal products that are toxic to both animals and plants. Their importance in the pathogenicity of Fusarium spp. on crop plants has inspired efforts to understand the genetic and biochemical mechanisms leading to trichothecene synthesis. In order to better understand T-2 toxin biosynthesis by Fusarium sporotrichioides and DON biosynthesis by F. graminearum, we compared the nucleotide sequence of the 23-kb core trichothecene gene cluster from each organism. This comparative genetic analysis allowed us to predict proteins encoded by two trichothecene genes, TRI9 and TRI10, that had not previously been described from either Fusarium species. Differences in gene structure also were correlated with differences in the types of trichothecenes that the two species produce. Gene disruption experiments showed that F. sporotrichioides TRI7 (FsTRI7) is required for acetylation of the oxygen on C-4 of T-2 toxin. Sequence analysis indicated that F. graminearum TRI7 (FgTRI7) is nonfunctional. This is consistent with the fact that the FgTRI7 product is not required for DON synthesis in F. graminearum because C-4 is not oxygenated.

Phylogenetic species recognition and species concepts in fungi

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.