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

Abstract

Background: The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions within those genes. Phylogenetic analyses have demonstrated a great deal of diversity which is reflected in the differing number of clades identified: 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. Such differing views have continued to confuse users of these taxonomies. Results: The phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole genome, nuclear genes, and mitochondrial genome sequences. The phylogenies were concordant except for three isolates. There were three concordant clades from all the phylogenies suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. Applying a multispecies coalescent (MSC) model on the eight single copy nuclear protein coding genes from the nuclear gene dataset concluded that the three concordant clades correspond to three phylogenetic species within the FOSC. There was 100% posterior probability support for the formation of three species within the FOSC. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex. The findings from this study were compared with previously published phylogenetics and species delimitation studies. 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.

Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

“…Following the most common species concept used in fungi, the Phylogenetic Species Concept (PSC) [ 6 ], a species is assigned to a phylogenetic cluster that shares a most recent common ancestor, and it differs phenotypically from its closest relatives [ 8 , 10 ]. However, this is not always observed in the genus Diaporthe , as in the case of the Diaporthe eres complex, which was shown in this study to display little or no morphological variation.…”

“…The Genealogical Concordance Phylogenetic Species Recognition (GCPSR), introduced by Taylor et al [ 6 ], relies in the comparison of individual gene genealogies to identify incongruences, and it has been particularly useful to delimit the species boundaries in morphologically conserved fungi [ 7 ]. However, the common approach of concatenating sequence data to delimit species without following the GCPSR principle [ 6 , 8 ] overestimates the true diversity of species, since each clade in combined trees is frequently recognized as a distinct lineage [ 9 , 10 ]. Moreover, species boundaries in closely related taxa can be somehow difficult to determine through multilocus sequence data, as some alleles are not expected to be reciprocally monophyletic in the initial stages of speciation, resulting in phylogenetic incongruences [ 7 , 11 ].…”

Characterization of Fusarium population associated with wilt of jojoba in Israel

“…However, associating VCGs to host specificity and virulence may be extrapolative, as multiple VCGs can be present in one pathogenic race or vice versa (Krnjaja et al, 2013). Using genealogical concordance phylogenetic species recognition, the FOSC has been phylogenetically reassessed rigorously and recently epitypified (Achari et al, 2020;Laurence et al, 2014;Lombard et al, 2019aLombard et al, , 2019bMaryani et al, 2019).…”

Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

“…pisi race 1 isolate RBG6462, race 2 isolate RBG6423, race 5 isolate RBG6425 and race 6 isolate RBG6418 were single spored as described by Burgess et al [ 99 ] and grown on Potato Dextrose Agar (PDA; Diffco Laboratories, Detroit) under dark incubation for 5 days at 25 °C before using them for preparing inoculum. An earlier study on the phylogenetic relationships of these isolates has placed RBG6462 in clade 3 while the other three isolates were in clade 2 within the FOSC [ 2 ]. Further analysis later predicted RBG6462 as ‘species’ 3 while the other three isolates were assigned as ‘species’ 2 within the FOSC [ 2 ].…”

“…pisi (Fop) causes vascular wilt in peas ( Pisum sativum ). Phylogenetic relationship study has shown that isolates of Fop races are polyphyletic and are present in clades 2 and 3 of the Fusarium oxysporum species complex (FOSC) [ 2 ].…”