Multiple Evolutionary Trajectories Have Led to the Emergence of Races in Fusarium oxysporum f. sp. lycopersici

Abstract

Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence of AVR1 in their genomes. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I. In FOL race 2 and race 3 isolates, AVR1 is absent, and hence they are virulent on tomato cultivars carrying I. In this study, we analyzed an approximately 100-kb genomic fragment containing the AVR1 locus of FOL race 1 isolate 004 (FOL004) and compared it to the sequenced genome of FOL race 2 isolate 4287 (FOL4287). A genomic fragment of 31 kb containing AVR1 was found to be missing in FOL4287. Further analysis suggests that race 2 evolved from race 1 by deletion of this 31-kb fragment due to a recombination event between two transposable elements bordering the fragment. A worldwide collection of 71 FOL isolates representing races 1, 2, and 3, all known vegetative compatibility groups (VCGs), and five continents was subjected to PCR analysis of the AVR1 locus, including the two bordering transposable elements. Based on phylogenetic analysis using the EF1-␣ gene, five evolutionary lineages for FOL that correlate well with VCGs were identified. More importantly, we show that FOL races evolved in a stepwise manner within each VCG by the loss of function of avirulence genes in a number of alternative ways.IMPORTANCE Plant-pathogenic microorganisms frequently mutate to overcome disease resistance genes that have been introduced in crops. For the fungus Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt in tomato, we have identified the nature of the mutations that have led to the overcoming of the I and I-2 resistance genes in all five known clonal lineages, which include a newly discovered lineage. Five different deletion events, at least several of which are caused by recombination between transposable elements, have led to loss of AVR1 and overcoming of I. Two new events affecting AVR2 that led to overcoming of I-2 have been identified. We propose a reconstruction of the evolution of races in FOL, in which the same mutations in AVR2 and AVR3 have occurred in different lineages and the FOL pathogenicity chromosome has been transferred to new lineages several times.

The multi-speed genome ofFusarium oxysporumreveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events

“…Moreover, it provides a means to escape “Muller’s ratchet” in mainly asexual species by exchanging at least parts of core chromosomes. The transposons that reside on pathogenicity chromosomes can play a role in fast adaptation to host-resistance, [19,74] probably mostly by mediating rearrangements [5,8,75], thus potentially disrupting modular genomic organizations and creating novel chromosome segments. Moreover, transposons may disperse into core chromosomes [76] where the chance of harmful effects of transposon insertion is larger than on dispensable chromosomes.…”

“…The occurrence of multiple almost identical sequences in a genome increases the likelihood of homologous recombination that can result in genome rearrangements or deletions [5], which can contribute to pathogen adaptation [1-3,6-15]. In addition, transposon insertion into an avirulence gene can result in regain of virulence [16-19]. If the avirulence gene is indispensable for infection the only option to escape recognition is to alter the amino acid sequence of the effector [20-22].…”

Pangenomic analysis reveals pathogen-specific regions and novel effector candidates inFusarium oxysporumf. sp.cepae

“…Previous studies have indicated that many other ff. spp., including Fol, have a polyphyletic origin 30 with some exhibiting clear patterns of 'race' evolution through stepwise loss of effectors 31 . All pathogenic Foc isolates formed a single clade, consistent with a single origin of pathogenicity on onion 12 .…”

Diminished Pathogen and Enhanced Endophyte Colonization upon CoInoculation of Endophytic and Pathogenic Fusarium Strains

“…The 10 µL qPCR mixture contained 10 ng of gDNA, 10 pM of each primer, and 2 µL of HOT FirePolEvaGreen qPCR Mix Plus (Solis BioDyne; Tartu, Estonia) were performed in QuantStudioTM3 (Thermo Scientific; Walthamm MA, USA). The cycling program was set to 15 min at 95 • C, 40 cycles of 15s at 95 • C, 1 min at 60 • C, and 30s at 72 • C. The melting curve analysis was performed afterwards as follows: 15s at 95 • C, 1 min at 60 • C, and 15s at 95 • C. The sequences of the primers used are summarized in Table S1 [26,27]. For InterGenic Spacer (IGS) primers two standard curves (four-or ten-times dilution) were performed with a starting concentration of 10 ng, resulting with a primer efficiently of 110 and 95%, respectively.…”

“…Fo strains within the same vegetative compatibility group (VCG) can form stable heterokaryons, while those belonging to different VCGs undergo cell death upon heterokaryon formation [29]. To test whether VCG incompatibility can result in a reduced viable concentration of Fol4287, and thereby reduce disease symptoms, two Fol strains of different VCG (Fol4287 (VCG030) and Fol017 (VCG031), [26]) were coinoculated. This resulted in disease symptoms that were indistinguishable from those observed upon single inoculation ( Figure S1c).…”