Phylogenetic relationship between the Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model. Phylogeneticanalysis of Fusarium oxysporum

Background: Fusarium oxysporum is a ubiquitous fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. It is a species complex (FOSC) of pathogenic and putatively non-pathogenic isolates. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions. Phylogenetic analyses from these studies have shown a great deal of diversity which is reflected in the different number of clades: three, five and eight. Genetic limitation within the species in the complex has been studied through Genealogical Concordance Phylogenetic Species Recognition (GCPSR) analyses with varying number of phylogenetic ‘species’ identified ranging from two to 21.Results: In this study, the phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole-genome sequence data, nuclear genes, and mitochondrial genome sequence data. The phylogenies were concordant except for three isolates. There were three concordant clades from the phylogenies of all three datasets, suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. The number of species within the FOSC was determined using the multispecies coalescent (MSC) model and the three concordant clades were designated as three species. There was 100% posterior probability support for the formation of three species within the FOSC using the nuclear gene dataset. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex.Conclusion: Phylogenetic analyses using three different gene datasets from Australian F. oxysporum isolates have all supported the formation of three major clades which delineated into three species. Species 2 (Clade 3) may be called F. oxysporum as it contains the neotype for F. oxysporum.