Association of Putative Fungal Effectors in Fusarium oxysporum with Wilt Symptoms in Soybean

BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche's Broom Disease in Cocoa

The fungus Moniliophthora perniciosa secretes protein effectors that manipulate the physiology of the host plant, but few effectors of this fungus have had their functions confirmed. We performed functional characterization of a promising candidate effector of M. perniciosa. The inoculation of rBASIDIN at 4 µmol L^-1 in the mesophyll of leaflets of Solanum lycopersicum caused symptoms of shriveling within 6 h without the presence of necrosis. However, when sprayed on the plant at a concentration of 11 µmol L^-1, it caused wilting symptoms only 2 h after application, followed by necrosis and cell death at 48 h. rBASIDIN applied to Theobroma cacao leaves at the same concentration caused milder symptoms. rBASIDIN caused hydrogen peroxide production in leaf tissue, damaging the leaf membrane and negatively affecting the photosynthetic rate of Solanum lycopersicum plants. Phylogenetic analysis indicated that BASIDIN has orthologs in other phytopathogenic basidiomycetes. Analysis of the transcripts revealed that BASIDIN and its orthologs are expressed in different fungal species, suggesting that this protein is differentially regulated in these basidiomycetes. Therefore, the results of applying BASIDIN allow the inference that it is an effector of the fungus M. perniciosa, with a strong potential to interfere in the defense system of the host plant.

First report of rootstalk rot of Hibiscus mutabilis caused by Fusarium oxysporum in China

H. Mutabilis (Cotton rose or confederate rose) is a deciduous shrub in the Malvaceae family, with ornamental, medicinal and edible values (Fan et al. 2015). In May to August 2020, 40.4% of potted plants of H. mutabilis were found to have root and stalk rot in Chengdu Botanical Garden (E104°7'28″, N30°45'57″). At first the leaves of affected H. mutabilis turned yellow and wilted, followed by the stem and root cortex became dark brown and rotten. Finally, the whole plant died within two months. Root and stem produced white mycelium when the humidity exceeded 90%. Samples taken from the lesions were surface disinfested for 3 min in 4% sodium hypochlorite, rinsed in sterile water and plated on potato dextrose agar (PDA), 35 single-spore cultures with similar morphology isolated from symptomatic tissues were obtained and subcultured. After seven days at 25°C in the dark, the mycelium of a representative culture MFR1 covered the entire plate surface (9 cm diameter). The aerial mycelium of cultures were white and fluffy at first and produced lavender pigment on the back of the cultures in the later stage. After seven days, the cultures produced abundant sickle-shaped macroconidia which have 3 to 5 septations and some oval or oblong microconidia which have 0 to 1 septation. Macroconidia 22.35~46.67 μm (mean 32.11 μm) in length and 4.32~7.72 μm (mean 5.21 μm) in width (n = 100). Microconidia 7.10~21.85 μm (mean 11.62 μm) in length and 2.76~6.84 μm (mean 4.20 μm) in width (n = 100). Based on these characteristics, isolates were tentatively identified as Fusarium sp. (Crous et al. 2021). Pathogenicity was tested on 1-year-old potted seedlings of H. mutabilis by root-zone irrigation inoculation in Sichuan Agricultural University (Jia et al.2019). Conidia suspension (1×107conidia/mL,collected from MFR1 )was poured into the soil along the plant roots. The same amount of distilled water was poured around the roots of the control plants. All inoculated and control plants were incubated in the greenhouse (about 25 ± 2°C). The experiment was performed three times. Within 25 days after inoculation, all plants inoculated with pathogens showed symptoms similar to those in the field, whereas the controls remained symptomless. The pathogen was reisolated from all inoculated plants, and the cultural and morphological characteristics were the same as those of the original isolate. After DNA extraction and PCR amplification, the translation elongation factor 1-alpha (TEF) and RNA polymerase II second largest subunit (RPB2) genes of a representative culture MFR1, were sequenced (O'Donnell et al. 2010) and deposited in GenBank (accession numbers OK334295 and ON316728, respectively). The TEF and RPB2 sequences were 99.7% and 99.39% identical to those of F. oxysporum (MN892354 and MZ198892). The result was confirmed by multilocus phylogenetic analysis. Through morphological identification and molecular analyses, the pathogen was identified as F. oxysporum. F. oxysporum is known to infect cotton (Dowd et al.2004), soybean (Ellis et al.2016) and banana (Fourie et al.2011) among other hosts, but it is the first report of F. oxysporum infecting H. mutabilis in China or worldwide. This disease seriously reduced the survival rate of H. mutabilis and may become an important reason to hinder the increase of H. mutabilis in potted seedlings stage. Moreover, the findings will provide theoretical basis to solve the bottleneck problem affecting the popularization and propagation of H. mutabilis.

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

BACKGROUND

Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 1920s. After successful management, it later re-emerged and by the 2000s comprised two separate epidemics on arabica coffee in Ethiopia and robusta coffee in east and central Africa.

RESULTS

Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks. Phylogenomic reconstruction using 13,782 single copy orthologs shows that the robusta population arose from the initial outbreak, whilst the arabica population is a divergent sister clade to the other strains. A screen for putative effector genes involved in pathogenesis shows that the populations have diverged in gene content and sequence mainly by vertical processes within lineages. However, 15 putative effector genes show evidence of horizontal acquisition, with close homology to genes from F. oxysporum. Most occupy small regions of homology within wider scaffolds, whereas a cluster of four genes occupy a 20Kb scaffold with strong homology to a region on a mobile pathogenicity chromosome in F. oxysporum that houses known effector genes. Lacking a match to the whole mobile chromosome, we nonetheless found close associations with DNA transposons, especially the miniature impala type previously proposed to facilitate horizontal transfer of pathogenicity genes in F. oxysporum. These findings support a working hypothesis that the arabica and robusta populations partly acquired distinct effector genes via transposition-mediated horizontal transfer from F. oxysporum, which shares coffee as a host and lives on other plants intercropped with coffee.

CONCLUSION

Our results show how historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with our efforts to resist them. Our list of putative effector genes identifies possible future targets for fungal control. In turn, knowledge of horizontal transfer mechanisms and putative donor taxa might help to design future intercropping strategies that minimize the risk of transfer of effector genes between closely-related Fusarium taxa.

Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems

In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar 'Happy Root' (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.

Association of Effector Six6 with Vascular Wilt Symptoms Caused by Fusarium oxysporum on Soybean

The Fusarium oxysporum species complex (FOSC) is a widely distributed group of fungi that includes both pathogenic and nonpathogenic isolates. In a previous study, isolates within the FOSC collected primarily from soybean were assessed for the presence of 12 fungal effector genes. Although none of the assayed genes was significantly associated with wilt symptoms on soybean, the secreted in xylem 6 (Six6) gene was present only in three isolates, which all produced high levels of vascular wilt on soybean. In the current study, a collection of F. oxysporum isolates from soybean roots and F. oxysporum f. sp. phaseoli isolates from common bean was screened for the presence of the Six6 gene. Interestingly, all isolates for which the Six6 amplicon was generated caused wilt symptoms on soybean, and two-thirds of the isolates showed high levels of aggressiveness, indicating a positive association between the presence of the effector gene Six6 and induction of wilt symptoms. The expression profile of the Six6 gene analyzed by quantitative reverse-transcription polymerase chain reaction revealed an enhanced expression for the isolates that caused more severe wilt symptoms on soybean, as established by the greenhouse assay. These findings suggest the suitability of the Six6 gene as a possible locus for pathogenicity-based molecular diagnostics across the various formae speciales.