A single gene in Fusarium oxysporum limits host range

Genomic Differences Between Two Fusarium oxysporum Formae Speciales Causing Root Rot in Cucumber

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.

Involvement of the SIX10 Gene in the Pathogenicity of Fusarium oxysporum Formae Speciales in Strawberries

Strawberries are planted globally as an important crop. Fusarium oxysporum f. sp. fragariae (Fof), a haploid mitosporic, pathogenic fungus with obvious host specificity, is responsible for an economically devastating soil-borne disease seriously threatening strawberry. Fusarium oxysporum is distributed in soils worldwide and causes vascular wilt and root rot disease in over 100 plant species. However, the formae speciales of F. oxysporum commonly have a very narrow host range, often restricted to a single host plant species. We isolated and identified pathogenic F. oxysporum from diseased strawberry samples collected from different provinces in China. Further analysis showed that among the 55 F. oxysporum isolates, only 70.91% belonged to Fof, and the remaining 29.09% were named Fo. The mycelial growth of Fof was faster than that of Fo at 20, 30, and 35 °C. The sporulation ability of Fof was weaker than that of Fo, and Fof presented a significantly higher germination rate under high temperatures. Fof and Fo from strawberry were not pathogenic to tomato or cucumber plants, and Fof showed significantly higher pathogenicity on strawberry than Fo. To explore the pathogenic mechanism of Fof, we knocked out SIX10 in Fof. The mycelial growth rate of ΔFofSIX10 was significantly slower than that of the wild type, but there were no significant differences in spore production. The pathogenicity of ΔFofSIX10 to strawberry was significantly weakened, showing decreased severity of symptoms, indicated by root and crown rot, and wilt. Our research provides a basis for understanding the interaction between F. oxysporum and the host strawberry and the occurrence and management of Fusarium disease on strawberry.

FONPS6, a Nonribosomal Peptide Synthetase, Plays a Crucial Role in Achieving the Full Virulence Potential of the Vascular Wilt Pathogen Fusarium oxysporum f. sp. Niveum

NPS6 is one of the nonribosomal peptide synthetase (NRPS) family members. The roles of NPS6 in ascomycetes are well known, but its roles in Fusarium oxysporum are unidentified. We investigated its function in the growth, morphology, stress sensitivity, allelochemical secretion, and pathogenesis in F. oxysporum (FoNPS6). The partial deletion of FoNPS6 orthologs (ΔFON-NPS6) resulted in hypersensitivity to H2O2 and KO2, iron depletion, and reduced virulence. Full virulence was restored by complementation. ΔFON-NPS6 not only inhibited spore formation but also displayed hyphal growth patterns that differed significantly from the wild-type strain. Plant leaching released allelochemicals, which FON-NPS6 broke down. All of these findings show that FoNPS6 quantitatively increases F. oxysporum's pathogenicity.

Identification and pathogenicity of Fusarium species associated with wilting and crown rot in almond (Prunus dulcis)

Severe Fusarium wilt and crown root symptoms were observed in almond orchards in Portugal. The present study elucidates the etiology of the disease through molecular, phenotypic, and pathogenic characterization. Three Fusarium isolates from Portugal were tested and 12 Fusarium isolates from almond from Spain were included for comparative purposes. Their identity was inferred by phylogenetic analysis combining tef1 and rpb2 sequences. The Portuguese isolates were identified as Fusarium oxysporum sensu stricto (s.s.), and the Spanish isolates as Fusarium nirenbergiae, F. oxysporum (s.s.), Fusarium proliferatum, Fusarium redolens (s.s.), Fusarium sambucinum (s.s.), and Fusarium sp. Fungal colonies and conidia were characterized on potato dextrose agar (PDA) and on Synthetischer Nährstoffarmer agar, respectively. The colonies had a variable morphology and their color ranged from white to pale violet. Typical Fusarium micro- and macroconidia were characterized. Temperature effect on mycelial growth was evaluated on PDA from 5 to 35 °C, with optimal growth temperature ranging between 16.8 and 26.4 °C. The pathogenicity of F. oxysporum was demonstrated by inoculating almond plants ('Lauranne') grafted on GF-677 or Rootpac 20 rootstocks. A significant reduction in plant growth, wilting, and xylem discoloration was observed, with Rootpac 20 being more susceptible than GF-677. Infections were also reproduced using naturally infested soils. Almond plants ('Lauranne') were inoculated with isolates of all Fusarium species, with F. redolens from Spain and F. oxysporum from Portugal being the most aggressive.

Transcriptomic-Proteomic Analysis Revealed the Regulatory Mechanism of Peanut in Response to Fusarium oxysporum

Peanut Fusarium rot, which is widely observed in the main peanut-producing areas in China, has become a significant factor that has limited the yield and quality in recent years. It is highly urgent and significant to clarify the regulatory mechanism of peanuts in response to Fusarium oxysporum. In this study, transcriptome and proteome profiling were combined to provide new insights into the molecular mechanisms of peanut stems after F. oxysporums infection. A total of 3746 differentially expressed genes (DEGs) and 305 differentially expressed proteins (DEPs) were screened. The upregulated DEGs and DEPs were primarily enriched in flavonoid biosynthesis, circadian rhythm-plant, and plant-pathogen interaction pathways. Then, qRT-PCR analysis revealed that the expression levels of phenylalanine ammonia-lyase (PAL), chalcone isomerase (CHI), and cinnamic acid-4-hydroxylase (C4H) genes increased after F. oxysporums infection. Moreover, the expressions of these genes varied in different peanut tissues. All the results revealed that many metabolic pathways in peanut were activated by improving key gene expressions and the contents of key enzymes, which play critical roles in preventing fungi infection. Importantly, this research provides the foundation of biological and chemical analysis for peanut disease resistance mechanisms.

Genetic Diversity and Population Structure of Fusarium oxysporum f. sp. conglutinans Race 1 in Northern China Samples

Fusarium oxysporum f. sp. conglutinans (FOC), the causal agent of cabbage fusarium wilt, is a serious threat to cabbage production in northern China, and most Chinese FOC isolates were identified as FOC race 1 (FOC1). To better understand the genetic diversity of FOC1 in northern China, we collected FOC isolates from five provinces in northern China and identified them as FOC1 through pathogenicity and race test. To evaluate the genome-level diversity of FOC1, we performed a genome assembly for a FOC1 isolate (FoYQ-1) collected from Yanqing, Beijing, where cabbage fusarium wilt was first reported in China. Using resequencing data of FOC1 isolates, we conducted a genome-wide SNP (single nucleotide polymorphism) analysis to investigate the genetic diversity and population structure of FOC1 isolates in northern China. Our study indicated that Chinese FOC1 can be grouped into four populations and revealed that the genetic diversity of FOC1 were closely associated with geographical locations. Our study further suggests that genetic differentiation occurred when FOC1 spread to the northwest provinces from Beijing Province in China. The FOC1 genetic diversity based on whole-genome SNPs could deepen our understanding of FOC1 variation and provide clues for the control of cabbage fusarium wilt in China.

Pathotypes of Fusarium oxysporum f. sp. fragariae express discrete repertoires of accessory genes and induce distinct host transcriptional responses during root infection

Convergent evolution of phytopathogenicity is poorly described, especially among multiple strains of a single microbial species. We investigated this phenomenon with genetically diverse isolates of Fusarium oxysporum f. sp. fragariae (Fof) that cause one of two syndromes: chlorosis and wilting (the 'yellows-fragariae' pathotype), or only wilting (the 'wilt-fragariae' pathotype). We challenged strawberry (Fragaria × ananassa) plants to root infection by five fungal isolates: three yellows-fragariae, one wilt-fragariae and one that is not pathogenic to strawberry. All Fof isolates had chromosome-level assemblies; three were newly generated. The two pathotypes triggered distinct host responses, especially among phytohormone-associated genes; yellows-fragariae isolates strongly induced jasmonic acid-associated genes, whereas the wilt-fragariae isolate primarily induced ethylene biosynthesis and signalling. The differentially expressed genes on fungal accessory chromosomes were almost entirely distinct between pathotypes. We identified an ~150 kbp 'pathogenicity island' that was horizontally transferred between wilt-fragariae strains. This predicted pathogenicity island was enriched with differentially expressed genes whose predicted functions were related to plant infection, and only one of these genes was also upregulated in planta by yellows-fragariae isolates. These results support the conclusion that wilt- and yellows-fragariae cause physiologically distinct syndromes by the expression of discrete repertoires of genes on accessory chromosomes.

Determining why continuous cropping reduces the production of the morel Morchella sextelata

Artificial cultivation of Morchella sextelata and other morels is expanding in China, but continuous cropping reduces Morchella for unknown reasons. Here, we investigated soil that had been used or not used for M. sextelata cultivation for 0, 1, and 2 years. We found that the continuous cropping of M. sextelata substantially reduced the pH and the nutrient content of the hyphosphere soil and increased sclerotia formation by M. sextelata. Changes in the structure of bacterial and fungal communities were associated with levels of available nitrogen (N) and phosphorus in the soil. With continuous cropping, the richness and diversity of fungal and bacterial communities increased, but the abundance of Bacillus and Lactobacillus decreased and the abundance of pathogenic fungi increased. FAPROTAX analysis indicated that N cycle functions were enriched more with than without continuous cultivation, and that enrichment of N cycle and sulfate respiration functions was higher in the second than in the first year of cultivation. FunGuild analysis indicated that the functions related to pathotrophs and wood saprotrophs were enriched by M. sextelata cultivation. Overall, the results suggest that continuous cropping may reduce M. sextelata production by acidifying the soil and increasing the abundance of pathogenic fungi. Additional research is needed to determine whether increases in the abundance of pathogenic fungi and changes in soil chemistry result in the declines in production that occur with continuous M. sextelata cultivation.

The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum

Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.

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.