A Polyphasic Approach Reveals Novel Genotypes and Updates the Genetic Structure of the Banana Fusarium Wilt Pathogen.

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed.

Phylogenetic and Biological Characterization of Fusarium oxysporum Isolates Associated with Onion in South Africa.

Fusarium oxysporum f. sp. cepae causes Fusarium basal rot of onion, a disease of worldwide importance. Limited information is available on the phylogenetic diversity, vegetative compatibility groups (VCGs), mating type idiomorphs, and virulence of F. oxysporum isolates associated with onion. Therefore, these characteristics were investigated in 19 F. oxysporum f. sp. cepae isolates from Colorado, 27 F. oxysporum f. sp. cepae and 33 F. oxysporum isolates nonpathogenic to onion from South Africa. Six F. oxysporum f. sp. cepae VCGs (0421 to 0426) were identified, of which three were new. The dominant VCGs in Colorado and South Africa were VCG 0421 (47% of isolates) and VCG 0425 (74%), respectively. VCG 0423 was the only VCG that was shared between the two regions. Molecular phylogenies (intergenic spacer region of the rDNA, elongation factor 1α, and mitochondrial small-subunit) confirmed the polyphyletic nature of F. oxysporum f. sp. cepae and showed that some F. oxysporum f. sp. cepae and nonpathogenic F. oxysporum isolates were genetically related. Most F. oxysporum f. sp. cepae isolates clustered into two distinct, well-supported clades. The largest clade only contained highly virulent isolates, including the two main VCGs (0421 and 0425), whereas the basal clade mostly contained moderately virulent isolates. These groupings along with the VCG data provide an important basis for selection of isolates for use in breeding programs, and for the development of molecular makers to identify VCGs. Mating type genotyping revealed the distribution of both mating type (MAT1-1 and MAT1-2) idiomorphs across phylogenetic clades, and the fact that several isolates contained both idiomorphs.

Molecular analyses of Pythium irregulare isolates from grapevines in South Africa suggest a single variable species.

The Pythium irregulare species complex is the most common and widespread Pythium spp. associated with grapevines in South Africa. This species complex has been subdivided into several morphological and phylogenetic species that are all highly similar at the sequence level [internal transcribed spacer (ITS) and cytochrome c oxidase (cox) regions]. The complex includes Pythium regulare and Pythium cylindrosporum, which are morphologically distinct, and P. irregulare sensu stricto (s.s.) and Pythium cryptoirregulare, which are morphologically similar. The aim of the current study was to determine whether 50 South African grapevine P. irregulare isolates represented more than one phylogenetically distinct species. The isolates were characterised using nuclear (ITS and ß-tubulin) and mitochondrial (cox1 and cox2) gene region phylogenies and two isozyme loci [glucose-6-phosphate isomerase (Gpi) and malate dehydrogenase (Mdh-1)]. Some of the gene sequence data were difficult to interpret phylogenetically, since some isolates contained two or more polymorphic ITS copies within the same isolate (intra-isolate variation) that clustered into different ITS sub-clades, i.e. the P. irregulare s.s. and P. cryptoirregulare sub-clades. The molecular data furthermore only revealed the presence of one phylogenetic species, P. irregulare. Morphological analyses of a subset of the isolates confirmed that the isolates were P. irregulare, and further showed that the P. cylindrosporum ex-type strain formed typical P. irregulare oogonia, and not the previously reported distinct elongated oogonia. Some of the molecular analyses suggested the occurrence of outcrossing events and possibly the formation of aneuploids or polyploids since (i) the nuclear and mitochondrial gene data sets were incongruent, (ii) polymorphic ITS copies were present within the same isolate, (iii) heterozygosities were observed in the ß-tubulin gene and Gpi and Mdh-1 loci in some isolates and (iv) more than two ß-tubulin alleles were detected in some isolates. Altogether, the data suggest that P. irregulare, P. cryptoirregulare, P. cylindrosporum, and possibly P. regulare should be synonimised under the name P. irregulare.

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.

Romellia is congeneric with Togninia, and description of Conidiotheca gen. nov. for one species of this genus with polysporous asci.

During a continued survey of fungi accommodated in the Calosphaeriales, we observed that the genus Romellia is morphologically heterogeneous. Historically, four species were placed in the genus. Romellia was introduced for taxa with globose, dark, superficial, papillate perithecia, a paraphysate centrum, and octosporous asci containing eight allantoid, hyaline ascospores. The type species, R. vibratilis, was revised in our study, and its freshly collected material was cultured. The anamorph obtained in vitro matches the generic concept of the hyphomycete genus Phaeoacremonium, the anamorph of Togninia. The phylogenies inferred from newly obtained sequences of LSU rDNA, beta-tubulin, and actin of R. vibratilis revealed that the species is congeneric with Togninia (Togniniaceae) and represents a good species. Revision of type and herbarium material of other Romellia species confirmed they are not congeneric with Togninia. Romellia tympanoides possesses immersed, subglobose perithecia with sessile asci containing eight ascospores, which during maturation produce ascoconidia filling the entire ascus. This maturation process represents a new kind of apparent polyspory known in the ascomycetes. We introduce a new genus, Conidiotheca, and a new combination for R. tympanoides. The species is compared with the genera Barrina and Tympanis. The relationships of two other Romellia species, R. ambigua and R. cornina, lie with Wegelina and Jattaea of the Calosphaeriales.

Phaeoacremonium krajdenii, a cause of white grain eumycetoma.

We describe the first case of white grain pedal eumycetoma caused by Phaeoacremonium krajdenii in a 41-year-old man from Goa, India. Based on histological examination of biopsy tissue showing serpentine granules, a culture of the granules yielding phaeoid fungal colonies, and morphological characteristics and sequence comparison of the partial beta-tubulin gene with the ex-type isolate of P. krajdenii, the causal agent was identified as P. krajdenii.