Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum

Poly(ADP-ribose) polymerase FonPARP1-catalyzed PARylation of protein disulfide isomerase FonPdi1 regulates pathogenicity of Fusarium oxysporum f. sp. niveum on watermelon

Poly(ADP-ribosyl)ation (PARylation), catalyzed by poly(ADP-ribose) polymerases (PARPs) and hydrolyzed by poly(ADP-ribose) glycohydrolase (PARG), is an important reversible post-translational protein modification in all eukaryotes, including plant pathogenic fungi. Previously, we revealed that FonPARP1, an active PARP, is crucial for the pathogenicity of Fusarium oxysporum f. sp. niveum (Fon), the causative agent of watermelon Fusarium wilt. This study explores the enzymatic activity and substrates of FonPARP1 in regulating Fon pathogenicity. FonPARP1 is localized in nuclei of Fon macroconidia and hyphae. Essential conserved domains and a key glutamic acid residue at position 729 are critical for FonPARP1 enzyme activity and pathogenicity function in Fon. FonPARP1 interacts with protein disulfide isomerase FonPdi1 and PARylates it at 13 glutamic acid residues, affecting the interaction ability, PDI activity, ER homeostasis, and pathogenicity function. FonPARG1, interacting with both FonPARP1 and FonPdi1, hydrolyzes poly(ADP-ribose) chains from auto-PARylated FonPARP1 and FonPARP1-PARylated FonPdi1. These findings underscore the role of FonPARP1-catalyzed PARylation in regulating Fon pathogenicity and its significance in plant pathogenic fungi.

Molecular Characterization of Fusarium Isolates from Upland Cotton Roots in Uzbekistan and Whole-Genome Comparison with Isolates from the United States

Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant cotton (Gossypium spp.) pathogen causing vascular wilt, browning of the vascular tissues, and plant death in the most severe cases. This global disease is responsible for sizeable crop losses annually and is found in many cotton-producing regions, including the Republic of Uzbekistan and the United States. Specifically, FOV race 4 (FOV4) has been disrupting production for years. This study aimed to genetically characterize FOV4 isolates causing disease in the main cotton-producing region of Uzbekistan and compare them with FOV4 isolates from the United States. A field study conducted in the Bukhara region of the Republic of Uzbekistan in the spring of 2022 identified both FOV4 and new Fusarium isolates from Upland cotton exhibiting typical Fusarium wilt symptoms. Molecular markers were initially used to identify isolates of interest, and a phylogenetic analysis was performed using partial EF1-α sequences, followed by a comparative genomic analysis. We also report for the first time the isolation of F. solani and F. commune causing Fusarium wilt in Uzbekistan. Furthermore, we show that the FOV4 population within our sampling region of Uzbekistan may be dominated by a single biotype with an effector profile similar to that of FOV race 7. One of these effector proteins is also present in the F. commune isolate showing virulence to cotton. Whole-genome comparisons between FOV races can identify unique genetic markers for FOV4 and aid in the development of tools for breeding FOV-resistant cotton varieties.

Characterization, Genome Sequencing, and Development of a Rapid PCR Identification Primer for Fusarium oxysporum f. sp. crocus, a New forma specialis Causing Saffron Corm Rot

Saffron corm rot (SCR), the most serious disease affecting saffron, has been confirmed to be caused by Fusarium oxysporum in previous studies. Compared to other fungal species, F. oxysporum exhibits host specialization, a special phenomenon associated with the secreted in xylem (SIX) genes. This study examined the pathogenicity specialization of F. oxysporum isolated from saffron corms with SCR disease. The results showed that this F. oxysporum strain was strongly pathogenic to saffron corms, causing SCR; weakly pathogenic to the corms of freesia, which is in the Iridaceae family along with saffron; and not pathogenic to watermelon, melon, and tomato. Other formae speciales of F. oxysporum were not pathogenic to saffron corms. This suggests that F. oxysporum saffron strains exhibit obvious pathogenicity specialization for Iridaceae spp. Subsequently, the F. oxysporum saffron strain (XHH35) genome was sequenced, and a comparative genomics study of XHH35 and three other formae speciales was conducted using OrthoVenn3. XHH35 contained 90 specific genes absent in the other three formae speciales. These genes are involved in certain key biological processes and molecular functions. Based on BLAST homology searching, the F. oxysporum saffron strain (XHH35) genome was predicted to contain seven SIX genes (SIX 4, SIX 6, SIX 7, SIX 10, SIX 11, SIX 12, and SIX 14) highly homologous to F. oxysporum f. sp. lycopersici, which was verified using polymerase chain reaction (PCR) amplification. The corresponding individual phylogenetic tree indicated that the F. oxysporum saffron strain (XHH35) showed a separate branch with different formae speciales. This study is the first-ever report of F. oxysporum f. sp. crocus, a new forma specialis. Based on the specificity of its SIX genes, the SIX 10 gene was selected to further establish a rapid identification technique for F. oxysporum f. sp. crocus, which will be useful in future research.

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses. Notably, homologues of Secreted in Xylem (SIX) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed.

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana)

Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.

Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.

Functional Genomics and Comparative Lineage-Specific Region Analyses Reveal Novel Insights into Race Divergence in Verticillium dahliae

Verticillium dahliae is a widespread soilborne fungus that causes Verticillium wilt on numerous economically important plant species. In tomato, until now, three races have been characterized based on the response of differential cultivars to V. dahliae, but the genetic basis of race divergence in V. dahliae remains undetermined. To investigate the genetic basis of race divergence, we sequenced the genomes of two race 2 strains and four race 3 strains for comparative analyses with two known race 1 genomes. The genetic basis of race divergence was described by the pathogenicity-related genes among the three races, orthologue analyses, and genomic structural variations. Global comparative genomics showed that chromosomal rearrangements are not the only source of race divergence and that race 3 should be split into two genotypes based on orthologue clustering. Lineage-specific regions (LSRs), frequently observed between genomes of the three races, encode several predicted secreted proteins that potentially function as suppressors of immunity triggered by known effectors. These likely contribute to the virulence of the three races. Two genes in particular that can act as markers for race 2 and race 3 (VdR2e and VdR3e, respectively) contribute to virulence on tomato, and the latter acts as an avirulence factor of race 3. We elucidated the genetic basis of race divergence through global comparative genomics and identified secreted proteins in LSRs that could potentially play critical roles in the differential virulence among the races in V. dahliae.

IMPORTANCE Deciphering the gene-for-gene relationships during host-pathogen interactions is the basis of modern plant resistance breeding. In the Verticillium dahliae-tomato pathosystem, two races (races 1 and 2) and their corresponding avirulence (Avr) genes have been identified, but strains that lack these two Avr genes exist in nature. In this system, race 3 has been described, but the corresponding Avr gene has not been identified. We de novo-sequenced genomes of six strains and identified secreted proteins within the lineage-specific regions (LSRs) distributed among the genomes of the three races that could potentially function as manipulators of host immunity. One of the LSR genes, VdR3e, was confirmed as the Avr gene for race 3. The results indicate that differences in transcriptional regulation may contribute to race differentiation. This is the first study to describe these differences and elucidate roles of secreted proteins in LSRs that play roles in race differentiation.

Effects of Fengycins and Iturins on Fusarium oxysporum f. sp. physali and Root Colonization by Bacillus velezensis Bs006 Protect Golden Berry Against Vascular Wilt

Bacillus velezensis Bs006 has shown antagonistic activity on Fusarium oxysporum f. sp. physali and biocontrol activity against Fusarium wilt (FW) in golden berry (Physalis peruviana). We hypothesized that strain Bs006 has the ability to synthesize antimicrobial cyclic lipopeptides (CLPs) like other members of the same species. However, if so, the real effects of CLPs on F. oxysporum f. sp. physali and their potential as a biocontrol tool against Physalis-FW have not been elucidated. In this study the CLPs profile of Bs006 in liquid culture and antagonist-plant-pathogen interactions were characterized. Also, the potential effects of supernatant free of bacteria against F. oxysporum f. sp. physali and FW were explored and compared with the effects of pure CLPs. Ultraperformance liquid chromatography-electrospray ionization-mass spectrometry analysis revealed the capacity of Bs006 to synthesize homologous compounds of iturins, surfactins, and fengycins in liquid culture and on the inhibition zone against F. oxysporum f. sp. physali in dual confrontation tests. Bs006 supernatant reduced the germination and growth of F. oxysporum f. sp. physali and caused vacuolization, swelling, and lysis of F. oxysporum f. sp. physali cells in a concentration-dependent manner. Pure fengycins affected the development of F. oxysporum f. sp. physali from 11 mg/liter and iturins from 21 mg/liter. In a gnotobiotic system, Bs006 colonized the root surface of golden berry, inhibited the growth of F. oxysporum f. sp. physali, and produced CLPs. Individual application of Bs006 and supernatant protected the plants from F. oxysporum f. sp. physali infections by 37 to 53%, respectively. Meanwhile, fengycins reduced the disease progress by 39%. These results suggest further studies to select an optimum combination of Bs006 and supernatant or CLPs, which might be a good option as biofungicide against F. oxysporum f. sp. physali.

Mixtures of Biological Control Agents and Organic Additives Improve Physiological Behavior in Cape Gooseberry Plants under Vascular Wilt Disease

This study aimed to assess the soil application of mixtures of biological control agents (BCAs) (Trichoderma virens and Bacillus velezensis) and organic additives (chitosan and burnt rice husk) on the physiological and biochemical behavior of cape gooseberry plants exposed to Fusarium oxysporum f. sp. physali (Foph) inoculum. The treatments with inoculated and non-inoculated plants were: (i) T. virens + B. velezensis (Mix), (ii) T. virens + B. velezensis + burnt rice husk (MixRh), (iii) T. virens + B. velezensis + chitosan (MixChi), and (iv) controls (plants without any mixtures). Plants inoculated and treated with Mix or MixChi reduced the area under the disease progress curve (AUDPC) (57.1) and disease severity index (DSI) (2.97) compared to inoculated plants without any treatment (69.3 for AUDPC and 3.2 for DSI). Additionally, these groups of plants (Mix or MixChi) obtained greater leaf water potential (~-0.5 Mpa) and a lower MDA production (~12.5 µmol g-2 FW) than plants with Foph and without mixtures (-0.61 Mpa and 18.2 µmol g-2 FW, respectively). The results suggest that MixChi treatments may be a promising alternative for vascular wilt management in cape gooseberry crops affected by this disease.

The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors

Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.

The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors

Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.

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

Cape gooseberry production has been limited by vascular wilt caused by Fusarium oxysporum f. sp. physali (Foph). Fusaric acid (FA) is a mycotoxin produced by many Fusarium species such as F. oxysporum formae speciales. The effects of the interaction between this mycotoxin and plants (such as cape gooseberry) under biotic stress (water deficit, WD) have been little explored. Three experiments were carried out. The objectives of this study were to evaluate (i) different Foph inoculum densities (1 × 104 and 1 × 106 conidia ml-1; experiment (1); (ii) the effect of times of exposure (0, 6, 9, and 12 h) and FA concentrations (0, 12.5, 25, 50, and 100 mg L-1; experiment (2), and (iii) the interaction between Foph (1 × 104 conidia mL-1) or FA (25 mg L-1 × 9 h), and WD conditions (experiment 3) on the physiological (plant growth, leaf stomatal conductance (g s ), and photochemical efficiency of PSII (Fv/Fm ratio) and biochemical [malondialdehyde (MDA) and proline] responses of cape gooseberry seedling ecotype Colombia. The first experiment showed that Foph inoculum density of 1 × 106 conidia ml-1 caused the highest incidence of the disease (100%). In the second experiment, g s (~40.6 mmol m-2 s-1) and Fv/Fm ratio (~0.59) decreased, whereas MDA (~9.8 μmol g-1 FW) increased in plants with exposure times of 9 and 12 h and an FA concentration of 100 mg L-1 compared with plants without FA exposure or concentrations (169.8 mmol m-2 s-1, 0.8, and 7.2 μmol g-1 FW for g s , Fv/Fm ratio and MDA, respectively). In the last experiment, the interaction between Foph or FA and WD promoted a higher area under the disease progress curve (AUDPC) (Foph × WD = 44.5 and FA × WD = 37) and lower g s (Foph × WD = 6.2 mmol m-2 s-1 and FA × WD = 9.5 mmol m-2 s-1) compared with plants without any interaction. This research could be considered as a new approach for the rapid scanning of responses to the effects of FA, Foph, and WD stress not only on cape gooseberry plants but also on other species from the Solanaceae family.

Secreted in Xylem Genes: Drivers of Host Adaptation in Fusarium oxysporum

Fusarium oxysporum (Fo) is a notorious pathogen that significantly contributes to yield losses in crops of high economic status. It is responsible for vascular wilt characterized by the browning of conductive tissue, wilting, and plant death. Individual strains of Fo are host specific (formae speciales), and approximately, 150 forms have been documented so far. The pathogen secretes small effector proteins in the xylem, termed as Secreted in Xylem (Six), that contribute to its virulence. Most of these proteins contain cysteine residues in even numbers. These proteins are encoded by SIX genes that reside on mobile pathogenicity chromosomes. So far, 14 proteins have been reported. However, formae speciales vary in SIX protein profile and their respective gene sequence. Thus, SIX genes have been employed as ideal markers for pathogen identification. Acquisition of SIX-encoding mobile pathogenicity chromosomes by non-pathogenic lines, through horizontal transfer, results in the evolution of new virulent lines. Recently, some SIX genes present on these pathogenicity chromosomes have been shown to be involved in defining variation in host specificity among formae speciales. Along these lines, the review entails the variability (formae speciales, races, and vegetative compatibility groups) and evolutionary relationships among members of F. oxysporum species complex (FOSC). It provides updated information on the diversity, structure, regulation, and (a)virulence functions of SIX genes. The improved understanding of roles of SIX in variability and virulence of Fo has significant implication in establishment of molecular framework and techniques for disease management. Finally, the review identifies the gaps in current knowledge and provides insights into potential research landscapes that can be explored to strengthen the understanding of functions of SIX genes.

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem

Vascular wilt, caused by the pathogen Fusarium oxysporum f. sp. physali (Foph), is a major disease of cape gooseberry (Physalis peruviana L.) in Andean countries. Despite the economic losses caused by this disease, there are few studies related to molecular mechanisms in the P. peruviana—Foph pathosystem as a useful tool for crop improvement. This study evaluates eight candidate genes associated with this pathosystem, using real-time quantitative PCR (RT-qPCR). The genes were identified and selected from 1,653 differentially expressed genes (DEGs) derived from RNA-Seq analysis and from a previous genome-wide association study (GWAS) of this plant-pathogen interaction. Based on the RT-qPCR analysis, the tubuline (TUB) reference gene was selected for its highly stable expression in cape gooseberry. The RT-qPCR validation of the candidate genes revealed the biological variation in their expression according to their known biological function. Three genes related to the first line of resistance/defense responses were highly expressed earlier during infection in a susceptible genotype, while three others were overexpressed later, mostly in the tolerant genotype. These genes are mainly involved in signaling pathways after pathogen recognition, mediated by hormones such as ethylene and salicylic acid. This study provided the first insight to uncover the molecular mechanism from the P. peruviana—Foph pathosystem. The genes validated here have important implications in the disease progress and allow a better understanding of the defense response in cape gooseberry at the molecular level. Derived molecular markers from these genes could facilitate the identification of tolerant/susceptible genotypes for use in breeding schemes.

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

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.

Putative Effector Genes Distinguish Two Pathogenicity Groups of Fusarium oxysporum f. sp. spinaciae

Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in F. oxysporum f. sp. spinaciae genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographically diverse F. oxysporum isolates was tested for pathogenicity on each of three spinach inbreds. Thirty-nine isolates identified as F. oxysporum f. sp. spinaciae caused quantitative differences in disease severity among the inbreds that revealed two distinct pathogenicity groups of F. oxysporum f. sp. spinaciae. Putative effector gene profiles, predicted from whole-genome sequences generated for nine F. oxysporum f. sp. spinaciae isolates and five nonpathogenic, spinach-associated F. oxysporum (NPS) isolates, distinguished the F. oxysporum f. sp. spinaciae isolates from the NPS isolates, and separated the F. oxysporum f. sp. spinaciae isolates into two groups. Five of the putative effector genes appeared to be unique to F. oxysporum f. sp. spinaciae, as they were not found in 222 other publicly available genome assemblies of F. oxysporum, implicating potential involvement of these genes in pathogenicity to spinach. In addition, two combinations of the 14 known Secreted in Xylem (SIX) genes that have been affiliated with host pathogenicity in other formae speciales of F. oxysporum were identified in genome assemblies of the nine F. oxysporum f. sp. spinaciae isolates, either SIX8 and SIX9 or SIX4, SIX8, and SIX14. Characterization of these putative effector genes should aid in understanding mechanisms of pathogenicity in F. oxysporum f. sp. spinaciae, developing molecular tools for rapid detection and quantification of F. oxysporum f. sp. spinaciae, and breeding for resistance to Fusarium wilt in spinach.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii

BACKGROUND

Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.

RESULTS

A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.

CONCLUSIONS

There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.

Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (H_E: 0.35 to 0.36 and F_IS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (F_ST: 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.

Screening of Different Physalis Genotypes as Potential Rootstocks or Parents Against Vascular Wilt Using Physiological Markers

Cape gooseberry (Physalis peruviana L.) is one of the most exported Andean fruits in Colombia. Vascular wilt caused by Fusarium oxysporum f. sp. physali (FOph) has led to a reduction in crop areas in recent years. Therefore, the aim of this study was to select genotypes with resistance to vascular wilt that can be useful as rootstocks from a group of six Physalis genotypes (Physalis ixocarpa, Physalis floridana, and Physalis peruviana genotypes Colombia, Sudafrica, Peru, and Accession 62) using physiological variables such as maximum quantum efficiency of Photosystem II (Fv/Fm), leaf gas exchange properties [net photosynthesis rate (Pn) and stomatal conductance (g s )], and leaf water potential. An experiment was carried out under greenhouse conditions in which plants of the different Physalis materials were inoculated with the F. oxysporum f. sp. physali strain Map5 at a concentration of 1 × 106 conidia mL-1. Physiological and disease development variables were measured at 15, 23, and 31 days after inoculation (DAI). The results obtained showed that P. peruviana genotypes Colombia and Sudafrica showed greater susceptibility to the disease (disease severity index 3.8 and 3.6, respectively). Net photosynthesis rate (Pn), stomatal conductance (g s ), water potential (Ψ fw ), and Fv/Fm ratio were lower compared to non-inoculated plants. P. floridana and P. ixocarpa plants inoculated with F. oxysporum showed similar behavior to non-inoculated plants for the evaluated variables. In conclusion, the results obtained suggest that these two genotypes can be considered in breeding programs or as rootstock for the establishment of cape gooseberry crops in soils with the presence of the pathogen.

Bioactive compounds induced in Physalis angulata L. by methyl-jasmonate: an investigation of compound accumulation patterns and biosynthesis-related candidate genes

We employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC-MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study.

Identification of Pathogenicity Groups and Pathogenic Molecular Characterization of Fusarium oxysporum f. sp. sesami in China

Fusarium oxysporum f. sp. sesami is an extremely destructive pathogen, causing sesame Fusarium wilt disease worldwide. To clarify the pathogenicity and the genetic characters of F. oxysporum f. sp. sesami, we systematically investigated 69 F. oxysporum isolates collected from major sesame-growing areas in China. Among these isolates, 54 isolates were pathogenic and 15 were nonpathogenic according to pathogenicity testing on sesame seedlings. For the pathogenic isolates, three F. oxysporum f. sp. sesami pathogenicity groups were defined based on the three differential sesame hosts for the first time. A translation elongation factor 1α gene tree was constructed to determine the genetic diversity of the F. oxysporum isolates but could not separate F. oxysporum f. sp. sesami isolates from the nonpathogenic isolates and other F. oxysporum formae speciales. Ten secreted-in-xylem (SIX) genes (one family of effectors) were identified in F. oxysporum f. sp. sesami isolates by a search with the genome data, and were subsequently screened in the 69 F. oxysporum isolates. Compared with the SIX gene profiles in other F. oxysporum formae speciales, the presence and sequence variations of the SIX gene homologs directly correlated with the specific pathogenicity of F. oxysporum f. sp. sesami toward sesame. Furthermore, eight of these F. oxysporum f. sp. sesami SIX genes were significantly expressed in sesame plants as infection of the F. oxysporum f. sp. sesami isolate. These findings have important significance for understanding the pathogenic basis of F. oxysporum f. sp. sesami isolates, and will contribute to improve the diagnostics to effectively control Fusarium wilt disease in sesame.

Physiological Response of Cape Gooseberry Seedlings to Three Biological Control Agents Under Fusarium oxysporum f. sp. physali Infection

Cape gooseberry (Physalis peruviana) fruit has gained recognition owing to its nutritional value and versatility to be consumed processed or as a fresh product. These characteristics have made it an important product in both national and international markets. One of the main limitations for this crop is Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. physalis, for which biological control is emerging as an alternative to conventional management with chemical synthesis products. However, information on the effect that biological control agents have on the growth and development of plants is scarce. In this research, the physiological response of cape gooseberry plants (stomatal conductance, leaf water potential, growth parameters, total chlorophyll, carotenoid, and proline and malondialdehyde contents) to the treatment with three potential biocontrol agents (BCAs) Trichoderma koningiopsis, Trichoderma virens, and Bacillus velezensis was determined. The study was conducted under greenhouse conditions; F. oxysporum was inoculated in the soil, and BCAs were soil drenched in the germination and transplanting stages. Plants inoculated with the pathogen and plants without inoculation were used as controls. It was found that the plants inoculated and treated with T. virens showed the lowest disease levels (area under the disease progress curve of 48.5 and disease severity index of 2.1). Additionally, they showed a lower water potential (-0.317 Mpa), a greater leaf area (694.7 cm²), and a higher stomatal conductance (110.3 mmol m^-2 s^-1) compared with the control. Consequently, it can be concluded that T. virens can be a good candidate for the management of Fusarium wilt in the cape gooseberry crop.

Physiological Responses to the Foliar Application of Synthetic Resistance Elicitors in Cape Gooseberry Seedlings Infected with Fusarium oxysporum f. sp. physali

Vascular wilt caused by Fusarium oxysporum is the most limiting disease that affects cape gooseberry (Physalis peruviana L.) crops in Colombia. The use of synthetic elicitors for vascular wilt management is still scarce in Andean fruit species. The objective of the present study was to evaluate the effect and number of foliar applications of synthetic elicitors such as jasmonic acid (JA), salicylic acid (SA), brassinosteroids (BR), or a commercial resistance elicitor based on botanical extracts (BE) on disease progress and their effect on the physiology of cape gooseberry plants inoculated with F. oxysporum f. sp. physali. Groups of ten plants were separately sprayed once, twice, or three times with a foliar synthetic elicitor, respectively. Elicitor applications were performed at the following concentrations: JA (10 mL L⁻¹), SA (100 mg L⁻¹), BR (1 mL L⁻¹) and BE (2.5 mL of commercial product (Loker^®) L⁻¹). The results showed that three foliar BR, SA, or BE applications reduced the area under the disease progress, severity index, and vascular browning in comparison to inoculated plants without any elicitor spray. Three BR, SA, or BE sprays also favored stomatal conductance, water potential, growth (total dry weight and leaf area) and fluorescence parameters of chlorophyll compared with inoculated and untreated plants with no elicitor sprays. Three foliar sprays of SA, BR, or BE enhanced photosynthetic pigments (leaf total chlorophyll and carotenoid content) and proline synthesis and decreased oxidative stress in Foph-inoculated plants. In addition, the effectiveness of three foliar BR, SA, or BE sprays was corroborated by three-dimensional plot and biplot analysis, in which it can evidence that stomatal conductance, proline synthesis, and efficacy percentage were accurate parameters to predict Foph management. On the hand, JA showed the lowest level of amelioration of the negative effects of Foph inoculation. In conclusion, the use of the synthetic elicitors BR, SA, or BE can be considered as a tool complementary for the commercial management of vascular wilt in areas where this disease is a limiting factor.

Characterization of Pathogenic and Nonpathogenic Fusarium oxysporum Isolates Associated with Commercial Tomato Crops in the Andean Region of Colombia

In Colombia, tomato production under protected conditions represents an important economic contribution to the agricultural sector. Fusarium wilt diseases, caused by pathogenic formae speciales of the soil-borne fungus Fusarium oxysporum Schltdl., cause significant yield losses in tomatoes throughout the world. Investigation of the F. oxysporum-tomato pathosystem in Colombia is required to develop appropriate alternative disease management. In this study, 120 fungal isolates were obtained from four different departments in the Central Andean Region in Colombia from tomato crops with symptoms of wilt disease. A molecular characterization of the fungal isolates was performed using the SIX1, SIX3, and SIX4 effector genes of Fusarium oxysporum f. sp. lycopersici W.C. Snyder & H.N. Hansen (Fol). Additionally, we developed a new specific marker to distinguish between Fusarium oxysporum f. sp. radicis-lycopersici Jarvis & Shoemaker (Forl) and Fol isolates. Furthermore, a phylogenetic analysis using the Translation Elongation Factor 1-alpha (EF1a) gene was performed with the collected isolates. Two isolates (named Fol59 and Fol-UDC10) were identified as Fol race 2, four isolates were identified as Forl, six isolates were identified as F. solani, and most of the isolates were grouped within the F. oxysporum species complex. The phylogenetic tree of EF1a showed that most of the isolates could potentially correspond to nonpathogenic strains of F. oxysporum. Additional pathogenicity assays carried out with Fol59 and Fol-UDC10 confirmed that both isolates were highly virulent strains. This study represents a contribution to the understanding of the local interaction between tomatoes and F. oxysporum in Colombia.

Physiological, Biochemical and Chlorophyll Fluorescence Parameters of Physalis Peruviana L. Seedlings Exposed to Different Short-Term Waterlogging Periods and Fusarium Wilt Infection

Cape gooseberry has coped with abiotic and biotic stresses such as prolonged waterlogging periods and vascular wilt in recent years. The aim of this study was to evaluate the influence of four waterlogging periods on stomatal conductance (gs), leaf water potential (Ψwf), plant growth, leaf photosynthetic pigments, malondialdehyde (MDA) production, proline content and chlorophyll fluorescence parameters in cape gooseberry plants infected with Fusarium oxysporum f. sp. physali (Foph). Two-month-old ecotype “Colombia” plants were arranged in a completely randomized factorial design in eight treatments: plants without waterlogging (control), plants with waterlogging for 4, 6 and 8 d with and without Foph, respectively. The area under the disease progress curve was higher in inoculated plants subjected to 6 and 8 d of waterlogging (55.25 and 64.25) compared to inoculated plants but without waterlogging (45.25). The results also showed a lower plant growth, gs, Ψwf, leaf photosynthetic pigments and chlorophyll fluorescence parameters (Fv/Fm, electron transport rate (ETR), Y (II) and qP) as waterlogging periods in plants with Foph increased. However, this group of plants showed a greater proline and malondialdehyde (MDA) accumulation and a higher NPQ. In conclusion, cape gooseberry shows a low acclimation to waterlogging conditions of more than 6 d in soils with Foph.