Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineagespecific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae,

Fusarium is a large, complex genus that causes a wide variety of plant diseases, produces a number of mycotoxins and is becoming increasingly recognized as a significant human pathogen. These fungi occur in ecosystems in all parts of the globe, which makes them useful as a model to better understand biogeographic processes affecting the distribution of fungi. Here we review the information available on the biogeography of different species and clades of Fusarium and some of the likely processes affecting dispersal and speciation.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

No abstract

Fusarium wilt is a serious disease of the date palm Phoenix canariensis, caused by Fusarium oxysporum f. sp. canariensis (Foc). A previous study that characterized and compared the genetic diversity of the Australian Foc population with international strains suggested that the Australian population may have had an independent evolutionary origin. The current study compared the species phylogeny of the Australian and international populations and determined that Foc is not monophyletic, separating into three supported lineages across the two phylogenetic species of the Fusarium oxysporum species complex. This confirms an independent evolutionary origin for Foc in Australia. However, phylogenetic analysis of the putative pathogenicity genes Secreted In Xylem (SIX) did not reveal any separation of the Australian and international Foc strains. Furthermore, there was very low SIX sequence diversity within Foc. Horizontal gene transfer is argued to be the most parsimonious explanation for the incongruence between the species and SIX gene phylogenies.

Six new species of Fusarium associated with soil and plant hosts from ecosystems of minimal anthropogenic disturbance in Australia are described. Fusarium coicis from Coix gasteenii, F. goolgardi from Xanthorrhoea glauca, F. mundagurra from soil and Mangifera indica, F. newnesense from soil, F. tjaetaba from Sorghum interjectum and F. tjaynera from soil, Triodia microstachya, Sorghum interjectum and Sorghum intrans. Morphology and phylogenetic analysis of EF-1α, RPB1 and RPB2 sequence data were used to delineate species boundaries. The new species were phylogenetically distributed in the Fusarium sambucinum, F. fujikuroi, and F. chlamydosporum species complexes, and two novel species complexes. These six new species have particular phylogeographic significance as not only do they provide further insight into the geographic patterns of Fusarium evolution but also challenge current phylogeographic hypotheses.

Fusarium species associated with plants as pathogens, saprobes and endophytes in Australia are listed with notes on their pathogenicity and toxicity provided. A list of Fusarium species not known to occur in Australia also is provided and their quarantine significance evaluated.

Vanilla stem rot, caused by Fusarium oxysporum f. sp. vanillae (Fov), is the main constraint to increasing vanilla production in the major vanilla‐producing countries, including Indonesia. The current study investigated the origin of Fov in Indonesia using a multigene phylogenetic approach. Nineteen Fov isolates were selected to represent Indonesia, the Comoros, Mexico and Réunion Island. The translation elongation factor 1 alpha gene and the mitochondrial small subunit ribosomal RNA gene phylogenies resolved the Fov isolates into three distinct clades in both phylogenetic species of the F. oxysporum species complex, indicating a polyphyletic pattern of evolution. In addition, Fov isolates from Indonesia were also polyphyletic. These results suggest that the vanilla stem rot pathogen in Indonesia has a complex origin. The implications for disease management are discussed.