Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants

Abstract

The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A transcriptomic analysis of a highly virulent strain of F. oxysporum in cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other formae speciales (ff. spp.) of F. oxysporum. This pathogenic strain was classified as a new f. sp. named Foph, due to its specificity for cape gooseberry hosts. Here, we sequenced and assembled the genome of five strains of F. oxysporum from a fungal collection associated to the cape gooseberry crop (including Foph), focusing on the validation of the presence of SIX homologous and on the identification of putative effectors unique to Foph. By comparative and phylogenomic analyses based on single-copy orthologous, we found that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol that contain effector genes and identified six new putative effector genes, specific to Foph pathogenic strains. We also conducted a molecular characterization using this set of putative novel effectors in a panel of 36 additional stains of F. oxysporum including two of the four sequenced strains, from the fungal collection mentioned above. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified in this genomic analysis, represent new sources involved in the interaction between Foph and cape gooseberry, that could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.

Physiological Response of Cape Gooseberry Plants to Fusarium oxysporum f. sp. physali, Fusaric Acid, and Water Deficit in a Hydrophonic System

“…This finding fulfills one of the two conditions stated by Aducci et al ( 1997 ) to consider a toxin a disease determinant. In Foph, the presence of SIX (secreted in xylem) homologous and putative effectors clarified the interaction between Foph and cape gooseberry (Simbaqueba et al, 2021 ). In this study, mechanisms that contribute to Foph pathogenicity and virulence were elucidated.…”

“…According to the plant host, different formae speciales of this pathogen have been reported (Kant et al, 2011). Foph was reported in 2018 in cape gooseberry (Simbaqueba et al, 2018(Simbaqueba et al, , 2021. Foph causes disease symptoms such as chlorosis of lower leaves, plant wilting, leaf senescence, and, finally, plant death.…”

Alphafold-multimer predicts cross-kingdom interactions at the plant-pathogen interface

“…The other P69B inhibitor of Fo has previously been described as secreted-into-xylem protein-15 (FoSix15, Simbaqueba et al, 2021). FoSix15 uses a strand to occupy the S4, S2 and S1 pockets in P69B with tyrosine, leucine and asparagine residues with high confidence (Figure 5E).…”

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races ofFusarium oxysporumf.sp.lactucae

“…A further SIX gene, designated SIX15 was identified in the Fol genome following comparison with the F. oxysporum f. sp. physali (infects cape gooseberry) genome (Simbaqueba et al, 2021). Moreover, SIX gene complement and sequence can also vary between races within a single F. oxysporum f.sp.…”