Fusarium oxysporum f. sp. conglutinans, F. oxysporum f. sp. rapae, F. oxysporum f. sp. raphani, and F. oxysporum f. sp. matthiolae can cause yellows disease of economically important species in the Brassicaceae family. Among these, F. oxysporum f. sp. rapae induces yellows in leaf mustard and Chinese cabbage. SGE1 (secreted-in-xylem [SIX] gene expression 1) is a transcription factor characterized by the presence of the WOPR box domain. Homologs of SGE1 in other Fusarium species play a crucial role in virulence and regulate the expression of SIX effector genes. However, the role of the SGE1 homolog in F. oxysporum f. sp. rapae (FoRP-SGE1) in pathogenesis and fungal development remains unexplored. To investigate its function in regulating pathogenicity and fungal development, gene knockout mutants of FoRP-SGE1 (ΔFoRP-SGE1) were generated and validated. ΔFoRP-SGE1 showed a reduction in conidiation but normal colony growth and conidial germination. Notably, ΔFoRP-SGE1 completely lost pathogenicity in both leaf mustard and Arabidopsis thaliana, but it retained the ability to colonize leaf mustard plants, indicating that FoRP-SGE1 is a key pathogenicity factor. Expression of SIX9 and SIX14 was significantly diminished in ΔFoRP-SGE1. Furthermore, most chlamydospores of ΔFoRP-SGE1 lacked the outermost fibrillose coat. Germination of ΔFoRP-SGE1 chlamydospores was also impaired under various stress conditions, including osmotic stress, drought, UV exposure, and fluazinam toxicity. This study presents, for the first time, the role of a Fusarium SGE1 homolog in the morphology and persistence of chlamydospores. Collectively, our findings suggest that FoRP-SGE1 is a critical pathogenicity factor in the leaf mustard-F. oxysporum f. sp. rapae and Arabidopsis-F. oxysporum f. sp. rapae pathosystems and is involved in the development of the fibrillose coat of chlamydospores and their resistance to environmental stresses.

Fusarium basal rot (FBR) poses a serious threat to onion (Allium cepa L.) production worldwide. In South Korea, FBR is primarily associated with Fusarium oxysporum, F. commune, and F. proliferatum. To investigate the relationship between effector gene profiles and virulence, we screened 34 isolates collected from FBR-affected fields for 14 Secreted in Xylem (SIX) genes and three additional effector candidates (CRX1, CRX2, and C5). F. oxysporum isolates carrying the effector suite SIX3, SIX5, SIX7, SIX9, SIX10, SIX12, SIX14, together with CRX1, CRX2 and C5, exhibited significantly higher aggressiveness on onion seedlings and bulbs than effector-negative strains. Among F. commune isolates lacking SIX genes, those carrying both CRX1 and CRX2 tended to show greater pathogenicity than CRX-negative strains. Nevertheless, SIX-negative strains still caused substantial seedling loss and bulb-rot, indicating the involvement of SIX-independent virulence factors. All F. proliferatum isolates were comparably pathogenic to SIX-negative F. oxysporum and F. commune strains, and uniformly carried SIX2-1 and CRX2, with a subset also harboring the SIX2-2 homologue. Across all isolates, SIX9 was the most frequently detected SIX gene and was markedly enriched in strains exhibiting strong pathogenicity. We developed and validated a SIX9-targeted quantitative PCR (qPCR) assay that specifically detects SIX9-positive Fusarium isolates (mainly F. oxysporum and F. commune), with detection limits of 1 pg of DNA or 10⁴ conidia/g soil. These findings enhance our understanding of effector repertoires contributing to Fusarium pathogenicity on onion and provide a molecular tool to support FBR diagnosis.

ABSTRACTFusarium wilt, caused by Fusarium oxysporum f. sp. lactucae (Fol), poses a severe threat to butterhead lettuce (Lactuca sativa L.) production in Europe. New isolates have broken through resistance to Fol race 4 in existing lettuce cultivars. Pathogenicity tests on a differential cultivar set and genotyping revealed that the new isolates are variants of Fol race 4, designated here as race 4+. The new race differs in its profile of Secreted in Xylem (SIX) genes: while both races contain SIX9 and SIX14, only Fol race 4 contains SIX8. Fusarium spp. adapt quickly, which signals an urgent need to develop an effective integrated pest management (IPM) strategy for Fusarium wilt. Crop rotation can play a key role in this strategy, especially during warmer periods when Fol is most aggressive. Susceptibility to Fol races 4 and 4+ and root colonisation potential were assessed in various lettuce types and alternative vegetable crops. Most lettuce types showed either susceptibility or intermediate resistance, but coral lettuce was resistant. Most alternative crops were asymptomatic when grown in soil infested with both Fol 4 and Fol 4+ and also did not support root colonisation. However, in soil artificially infested with high Fol 4 concentrations, lamb's lettuce (Valerianella locusta) was symptomatic. In soil naturally infested with Fol 4 and Fol 4+, lamb's lettuce was asymptomatic, but latent growth of Fol 4 (and potentially Fol 4+) was observed at levels comparable to susceptible butterhead lettuce. The results suggest that effective management of Fusarium wilt during warmer periods could involve the cultivation of resistant alternative crops such as rocket or celery. During colder periods, a rotation of resistant coral lettuce cultivars may further reduce the disease pressure and allow the occasional culture of a susceptible butterhead lettuce cultivar.

The host specificity of Fusarium oxysporum (Fox) formae speciales has been reported to be linked to effector proteins known as Secreted in Xylem (SIX). These genes are associated with the non-autonomous mobile element miniature impala (mimp), normally distributed on the accessory chromosomes. The pattern of mimp associated with effector genes has been used to predict candidate effector profiles which characterize Fox formae speciales. In this study, we demonstrate the pathogenicity of strains Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407 and Fusarium oxysporum f.sp. radicis-cucumerinum (Forc) V03-2g in a common host plant (cucumber) and compare their genomes. The Forl ZUM2407 genome lacks SIX genes and their homologs, in contrast to Forc V03-2g. We predicted the total number of mimp elements in the genome of Forl ZUM2407 to be three-fold less than that of Forc V03-2g (10 and 36 copies, respectively). The mimp distribution pattern in Forl ZUM2407 was completely different from that present in Forc V03-2g. Candidate effector profile analysis did not predict that Forl ZUM2407 was able to infect cucumber plants like Forc V03-2g. Therefore, we assume that Forl ZUM2407 has a different type of genome organization associated with pathogenicity, whose effector profile cannot be described using the mimp-based approach.

Fusarium wilt of banana is a major production constraint in India, prompting banana growers to replace bananas with less remunerative crops. Effective disease management practices thus need to be developed and implemented to prevent further spread and damage caused by Fusarium oxysporum f. sp. cubense (Foc), the cause of Fusarium wilt. Currently, knowledge of disease incidence, affected varieties, and the geographical spread of Foc races in India are only scantily available. An extensive field survey was conducted in 53 districts of 16 major banana-growing states of and one union territory of India that covered both tropical and subtropical regions. Disease incidence ranged from 0 to 95% on farms, with Cavendish bananas (AAA) most affected. No Fusarium wilt symptoms due to Foc R1 were observed in Nendran (AAB) or Red Banana (AAA) in South India. During the survey, 293 Foc isolates were collected from Cavendish, Pisang Awak (ABB), Silk (AAB), Monthan (ABB), Neypoovan (AB), and Mysore (AAB) bananas. Isolate diversity was assessed through Vegetative Compatibility Group (VCG) analyses, sequencing of EF1α gene sequences, phylogenetic analyses, and characterisation by SIX gene composition. Thirteen VCGs were identified, of which VCGs 0124, 0125, 01220, and 01213/16 were dominant and infected Cavendish bananas. Phylogenetic analysis divided the Indian Foc isolates into race 1 (R1), subtropical race 4 (STR4), and tropical race 4 (TR4). Secreted in Xylem (SIX) gene analyses indicated that the effector genes SIX4 and SIX6 were present in the VCGs 0124, 0124/5, 0125, and 01220 of race 1, SIX7 was present only in Foc STR4, and SIX8 was found only in Foc R4 (TR4 and STR4) isolates. Insights into the geographical distribution of Foc races, and their interactions with banana varieties, can guide integrated disease management intervention strategies across India.

Given the criticalneed to preserve agricultural sustainability,there is an urgent call to address fungal infections. Our study presentsa promising approach by focusing on SIX (Secreted in Xylem) proteinsas a pivotal target for the development of innovative fungicidal strategies.Within the sphere of this study, we meticulously scrutinize the antifungalefficacy of our synthesized Cu(II) complex formulated as [Cu(L1)2(L2)]+(ClO4)−, whereL1 represents (E)-cyclohexyl–N(pyridine-2-xlmethylene) methanamine and L2H denotes cinnamic acid,compared against a commercially available fungicide comprising 4%hexaconazole and 68% zineb. Employing in silico methodologies, weundertake a comparative analysis targeting SIX proteins to discernthe potency of our compound. The X-ray diffraction, 1HNMR, and FTIR spectroscopic techniques were utilized to elucidatethe structure of the complex methodically. The lipophilicity testof the complex signifies its potential lipophilic nature and promptedfurther investigation into the complex’s interaction with DNA(DNA) and bovine serum albumin (BSA). The binding constant valuessuggested a notable interaction between the complex and both DNA andBSA. The antifungal test reveal that our complex emerges as a potentcontender in the battle against Fusarium equisetum (F.E.), exhibitinga commendable efficacy that positions it as a viable substitute forthe incumbent commercial fungicide. This discovery predicts well theprospect of bolstering agricultural resilience and safeguarding globalfood security in the face of pervasive fungal threats.

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.

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.

ABSTRACTRecent studies have shown numerous Fusarium spp. are associated with symptomatic conifer seedlings in both bareroot and container nursery systems. Some of these species have been found pathogenic to conifer seedlings (e.g., F. avenaceum, F. commune, F. oxysporum, F. solani, and F. verticillioides), but the mechanisms and shared evolutionary history of these conifer pathogenic species have not been well studied in these pathosystems. We compared whole genomes of 17 Fusarium spp. associated with conifer seedlings to elucidate putative shared pathogenicity/virulence gene profiles presumably expressed for roles in causing damping‐off and/or root disease of conifer seedlings. In addition, this work provides draft genomes of conifer‐associated Fusarium spp. and genomes not previously referenced in public databases (e.g., F. lactis, F. fredkrugeri, F. ipomoeae, and F. flocciferum). We identified pathogenicity/virulence genes associated with Fusarium spp. pathogens of conifers including effectors, the secreted in xylem (SIX) genes 2, 4, 9 and 14 and secondary metabolites, and the mycotoxins fumonisin and deoxynivalenol. We conclude that gene profiles are shared within Fusarium species complexes and among closely related Fusarium species complexes; however, these shared profiles are widely distributed across all Fusarium pathogens. These findings highlight potential targets for detecting and/or identifying Fusarium pathogens of conifers, but multiple methods and/or targets will be required depending on the species complexes and clades. More research is needed to determine the roles of expressed pathogenicity/virulence genes and the downstream metabolic products that result in pathogenesis to conifers.

New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes

Here, 12 Fusarium strains, previously described as F. oxysporum f. sp. cepae (Foc), were examined via multi-locus sequencing of calmodulin (cmdA), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1), to verify the taxonomic position of Foc in the newly established epitype of F. oxysporum. The strains in this study were divided into two clades: F. nirenbergiae and Fusarium sp. To further determine the host specifications of the strains, inoculation tests were performed on onion bulbs and Welsh onion seedlings as potential hosts. Four strains (AC145, AP117, Ru-13, and TA) isolated from diseased onions commonly possessed the secreted in xylem (SIX)-3, 5, 7, 9, 10, 12, and 14 genes and were pathogenic and highly aggressive to onion bulbs, whereas all strains except for one strain (AF97) caused significant inhibition of Welsh onion growth. The inoculation test also revealed that the strains harboring the SIX9 gene were highly aggressive to both onion and Welsh onion and the gene was expressed during infection of both onions and Welsh onions, suggesting the important role of the SIX9 gene in pathogenicity. This study provides insights into the evolutionary pathogenicity differentiation of Fusarium strains causing Fusarium basal rot and wilt diseases in Allium species.

Secreted in Xylem (SIX) are small effector proteins released by Fusarium oxysporum f.sp. cubense (Foc) into the plant's xylem sap disrupting the host's defence responses causing Fusarium wilt disease resulting in a significant decline in banana crop yields and economic losses. Notably, different races of Foc possess unique sets of SIX genes responsible for their virulence, however, these genes remain underutilized, despite their potential as biomarkers for early disease detection. Herein, we identified seven SIX genes i.e. SIX1, SIX2, SIX4, SIX6, SIX8a, SIX9a and SIX13 present in Foc Tropical Race 4 (FocTR4), while only SIX9b in Foc Race 1 (Foc1). Analysis of SIX gene expression in infected banana roots revealed differential patterns during infection providing valuable insights into host-pathogen interactions, virulence level, and early detection time points. Additionally, a comprehensive analysis of virulent Foc1_C2HIR and FocTR4_C1HIR isolates yielded informative genomic insights. Hence, these discoveries contribute to our comprehension of potential disease control targets in these plants, as well as enhancing plant diagnostics and breeding programs.

Fusarium wilt of lentil caused by Fusarium oxysporum f. sp. lentis (Fol) is a destructive pathogen limiting lentil production in India. In the present study, Secreted in Xylem (SIX) effectors genes were explored in Indian races of Fol and also a diagnostic tool for reliable detection of the disease was developed. Four SIX effectors genes, SIX11, SIX13, SIX6 and SIX2 were identified in 12 isolates of Fol belonging to seven races. SIX11 was present in all the races while SIX 13 was absent in race 6 and SIX6 was present only in race 4. The phylogenetic analysis revealed the conserved nature of the SIX genes within the forma specialis and showed sequence homology with F. oxysporum f. sp. pisi. The presence of three effectors, SIX11, SIX13 and SIX6 in race 4 correlates with high disease incidence in lentil germplasms. The in-silico characterization revealed the presence of signal peptide and localization of the effectors. Further SIX11 effector gene present in all the isolates was used to develop Fol-specific molecular marker for accurate detection. The marker developed could differentiate F. oxysporum f. sp. lycopersici, F. solani, F. oxysporum, Rhizoctonia solani and Sclerotium rolfsii and had a detection limit of 0.01ng μL- 1. The effector-based marker detection helps in the unambiguous detection of the pathogen under field conditions.

Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant-fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.

Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant–fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.

Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant–fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases in banana farming worldwide. Knowledge of the factors of genetic diversity and virulence of the pathogen contributes to the development of resistant cultivars and management strategies based on exclusion. In this study, phenotypic traits such as virulence and aggressiveness in a sample of 52 Foc isolates were analyzed and their relationship to the presence of putative effectors of gene SIX (Secreted in Xylem) pathogenicity homologs was verified. The similarity matrix revealed three isolates that were closest to the standard Foc race 1 strain. Isolates 229A and 218A were selected according to their aggressiveness profile in ‘Grand Naine’ and ‘Prata-Anã’, respectively, to replace the standard isolate of race 1 in the resistance screening process carried out by the breeding program. Two homologs of the SIX8 gene, SIX8a and SIX8b, are present in isolates of Foc from Brazil, and the SIX8b gene correlates with avirulence in the cultivar ‘Grand Naine’ (Cavendish). These results are important to support the banana genetic breeding program by identifying sources of resistance to Foc and contributing to the establishment of the function of SIX effector proteins.

There are four formae speciales of Fusarium oxysporum responsible for causing yellows of Brassicaceae. Because of crossbreeding among crops, the host ranges of these formae speciales often overlap, making pathogen identification a challenging task. Among these formae speciales, F. oxysporum f. sp. rapae and F. oxysporum f. sp. matthiolae still lack specific primers for pathogen identification. To address this problem, we targeted the secreted in xylem (SIX) genes, known as specific effectors of pathogenic F. oxysporum, for primer design. Through sequence comparison with other formae speciales, we successfully designed specific primers for F. oxysporum f. sp. rapae and F. oxysporum f. sp. matthiolae on SIX14 and SIX9, respectively. Both primer pairs exhibited high specificity in detecting F. oxysporum f. sp. rapae or F. oxysporum f. sp. matthiolae, distinguishing them from 20 nontarget formae speciales of F. oxysporum, five species of phytopathogenic Fusarium, and four other common pathogenic fungi affecting cruciferous plants. Moreover, the effectiveness of these specific primers was validated by detecting the pathogens in infected plants. To further enhance the identification process of the four formae speciales, we combined the two newly designed specific primer pairs with two previously published primer pairs, enabling the establishment of a multiplex PCR method that can accurately distinguish all four formae speciales of F. oxysporum responsible for causing yellows in cruciferous plants in a single reaction.

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.

Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.