Epitypification of Fusarium oxysporum – clearing the taxonomic chaos

Abstract

Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.

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

“…This shows that there is considerable genetic diversity in Australian F. oxysporum and this is in agreement with Laurence et al [18] who had five clades within the FOSC from natural ecosystems when using the same gene barcoding region as O'Donnell et al [16], whose isolates only grouped into three clades. Apart from Lombard et al [19] and Laurence et al [18] dataset, all other studies had three clades in the phylogenetic analyses. Greater genetic diversity within the Australian FOSC and Lombard et al [19] datasets could be due to convergent evolution of isolates with their hosts [52].…”

“…The diversity of the complex was studied by comparing the clades in the current study with previously published phylogenies. The combined dataset from the current study and Lombard et al [19] produced a phylogenetic tree with two clades ( Supplementary Fig. 7).…”

“…Testing the Lombard et al [19] dataset using the MSC model resulted in some well-supported nodes, depicted by species numbered 21, 17 and 9 ( Supplementary Fig. 9).…”

“…Laurence et al [30] used barcoding regions of eight genes (tef1-α, mtSSU, largest subunit of DNA-dependent RNA polymerase II (RPB1), RPB2, nitrate reductase (NIR), phosphate permease (PHO), calmodulin (cal), ATP citrate lyase(acl1) and predicted two 'species', while Brankovics et al [23] using the sequences of nine genes (γ-actin (act), cal, RPB2, tef1-α, tef3, 60Sribosomal protein L10 (rpl10a), topoisomerase I (top1), rDNA repeat and tub2) and the conserved part of the mitogenome predicted three 'species' which were concordant to the three clades in their phylogenetic analysis. Lombard et al [19] identified 21 'species' with no explanation of their model. GCPSR in the above studies was implemented in two steps as defined by Dettman et al [31] (i) identification of the independent evolutionary lineages (IEL) and (ii) exhaustive subdivision of isolates into phylogenetic species.…”

“…Clade 4 comprised of only Australian isolates. More recently, Lombard et al [19] identified eight clades within the FOSC using four barcoding gene regions, β-tubulin II (tub2), calmodulin (cal), the second largest subunit of DNA-dependent RNA polymerase II (RPB2) and tef-1α.…”