Martijn Rep

University of Amsterdam | UVA

Objective Wilt caused by Fusarium oxysporum f. sp. melonis (Fom) is one of the most widespread and destructive melon diseases worldwide. Whole-genome sequencing data of a diverse set of Fom strains, as well as several non-pathogenic strains isolated from melon from different parts of the world are described here. These data shed light on the geneti...

The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to...

The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to...

Understanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that...

With only a few exceptions, fungal effectors (small secreted proteins) have long been considered as species- or even isolate-specific. With the increasing availability of high-quality fungal genomes and annotations, trans-species or trans-genera families of effectors are being uncovered. Two avirulence effectors, AvrLm10A and AvrLm10B , of Leptosph...

The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investi...

Many plant pathogenic fungi contain conditionally dispensable (CD) chromosomes that are associated with virulence, but not growth in vitro. Virulence-associated CD chromosomes carry genes encoding effectors and/or host-specific toxin biosynthesis enzymes that may contribute to determining host specificity. Fusarium oxysporum causes devastating dise...

Fusarium oxysporum f. sp. melonis (Fom) is one of the most important pathogens of melon worldwide. In this study, we investigated the genomic diversity of Fom. One of the aims was to find clues for the origin(s) and dispersal of clonal lineages and races of Fom. We therefore included a large number of Fom strains from Iran, where melon has been cul...

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agr...

Fusarium oxysoporum f. sp. radicis‐cucumerinum (Forc) is able to cause disease in cucumber, melon, and watermelon, while F. oxysporum f. sp. melonis (Fom) can only infect melon plants. Earlier research showed that mobile chromosomes in Forc and Fom determine the difference in host range between Forc and Fom. By closely comparing these pathogenicity...

Fusarium oxysporum (Fo) is best known as a host‐specific vascular pathogen causing major crop losses. Most Fo strains, however, are root endophytes potentially conferring endophyte‐mediated resistance (EMR). EMR is a mechanistically poorly understood root‐specific induced resistance response induced by endophytic or nonhost pathogenic Fo strains. L...

Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae (Fos), is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in Fos genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographicall...

Many plant pathogenic fungi contain conditionally dispensable (CD) chromosomes that are associated with virulence, but not growth in vitro . Virulence-associated CD chromosomes carry genes encoding effectors and/or host-specific toxin biosynthesis enzymes that may contribute significantly to determining host specificity. Fusarium oxysporum causes d...

This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold Fusarium. Fusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members o...

Endophytic microbes conferring biocontrol are an eco-friendly alternative to control diseases in crops. Unfortunately, the use of endophytes to control diseases is not yet widespread as their application in agricultural settings is challenging and the outcome variable. Translating strains that perform well under laboratory conditions to the field p...

Fortunately, no fungus can cause disease on all plant species, and although some plant-pathogenic fungi have quite a broad host range, most are highly limited in the range of plant species or even cultivars that they cause disease in. The mechanisms of host specificity have been extensively studied in many plant-pathogenic fungi, especially in fung...

In Fusarium oxysporum f.sp. lycopersici, all effector genes reported so far – also called SIX genes – are located on a single accessory chromosome which is required for pathogenicity and can also be horizontally transferred to another strain. To narrow down the minimal region required for virulence, we selected partial pathogenicity chromosome dele...

Plant pathogens use effector proteins to promote host colonization. The mode of action of effectors from root invading pathogens, such as Fusarium oxysporum (Fo), is poorly understood. Here, we investigated whether Fo effectors suppress pattern‐triggered immunity (PTI), and whether they enter host cells during infection. ‐ Eight candidate effectors...

Root colonization by Fusarium oxysporum (Fo) endophytes reduces wilt disease symptoms caused by pathogenic Fo strains. The endophytic strain Fo47, isolated from wilt suppressive soils, reduces Fusarium wilt in various crop species such as tomato, flax, and asparagus. How endophyte-mediated resistance (EMR) against Fusarium wilt is achieved is uncle...

Fusarium oxysporum f. sp. radicis‐cucumerinum (Forc) causes severe root rot and wilt in several cucurbit species, including cucumber, melon, and watermelon. Previously, a pathogenicity chromosome, chrRC, was identified in Forc. Strains that were previously nonpathogenic could infect multiple cucurbit species after obtaining this chromosome via hori...

Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. He...

During host colonization, plant pathogenic fungi secrete proteins, called effectors, to facilitate infection. Collectively, effectors may defeat the plant immune system, but usually not all effectors are equally important for infecting a particular host plant. In Fusarium oxysporum f.sp. lycopersici , all known effector genes – also called SIX gene...

Environmental adaptation of organisms relies on fast perception and response to external signals, which lead to developmental changes. Plant cell growth is strongly dependent on cell wall remodeling. However, little is known about cell wall-related sensing of biotic stimuli and the downstream mechanisms that coordinate growth and defense responses....

This article is a Commentary on Sarkar et al., 224: 886–901.

[This corrects the article DOI: 10.3389/fmicb.2018.02977.].

Root endophytes can confer resistance against plant pathogens by direct antagonism or via the host by triggering induced resistance. The latter response typically relies on jasmonic acid (JA)/ethylene (ET)-depended signaling pathways, but can also be triggered via salicylic acid (SA)-dependent signaling pathways. Here, we set out to determine if en...

Rapid (co‐)evolution at multiple timescales is a hallmark of plant–microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights in genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathog...

Environmental adaptation of organisms relies on the fast perception and response to external signals, which leads to developmental changes. Plant cell growth is strongly dependent on cell wall remodeling. However, little is known about cell wall-related sensing of biotic stimuli and the downstream mechanisms that coordinate growth and immune respon...

Resistance (R) genes and endophytic organisms can both protect plants against pathogens. Although the outcome of both processes is the same, little is known about the commonalities and differences between both immune responses. Here we set out to phenotypically characterize both responses in the tomato-Fusarium pathosystem, and to identify markers...

EMR and RMR reduce susceptibility to Fusarium wilt (Fol007). (A) Ten-days-old seedlings of Fol007-susceptible KG52201 and Fol007-resistant KG324 were root dip-inoculated with water (mock), Fol007 or a mixture of Fo47:Fol007 (25 replicates for Fo47:Fol007 co-inoculated KG52201 and Fol007-inoculated KG324 seedlings, 10 replicates for the control trea...

Fo47 inoculation affects accumulation of specific proteins. (A) Proteins that were detected in at least three out of four replicates where labeled as present. Treatments embraced mock-inoculated, Fo47-inoculated, Fo47:Fol007-coinoculated and Fol007-inoculated C32 susceptible tomato plants. The black circle marks proteins that were specifically pres...

List of PR-5 proteins found in xylem sap of both bioassays. Uniprot IDs, names of the proteins, average of LFQ intensities for every treatment of the two bioassays, predicted location, GO category, disulphide bonds and length of the proteins are depicted in the table. LFQ values are represented in Log10 scale.

EMR and RMR reduce susceptibility to Fusarium wilt (Fol007). (A) Ten-days-old seedlings of Fol007-susceptible KG52201 and Fol007-resistant KG324 were root dip-inoculated with water (mock), Fol007 or a mixture of Fo47:Fol007 (25 replicates for Fo47:Fol007 co-inoculated KG52201 and Fol007-inoculated KG324 seedlings, 10 replicates for the control trea...

List of xylem sap proteins whose relative abundance changes upon co-inoculation of tomato with Fo47:Fol007 comparing to Fo47-inoculated.

Overview of the peptides matching NP24 and PR-5x proteins.

Fo47 colonizes tomato stems (A) To monitor stem colonization by Fo47 3-weeks-post-inoculation, stem sections at the crown and cotyledon-level were placed on PDA plates (10 replicates). Plates were scanned after 4 days of incubation. (B) Fungal outgrowth of the stem sections plotted as a percentage of infected sections. The experiment was repeated t...

Fol007 proteins identified and label-free quantified in Bioassay 1. LFQ values are in Log10 scale and 3,9 represent the LFQ cutoff.

Tomato proteins identified and label-free quantified in Bioassay 2. Samples labeled as ‘Mock’ for the water control, and ‘Patho’ for Fol007-inoculated KG324 resistant tomato plants. DAPs are marked with +. LFQ values are represented in Log10 scale. Sequence coverage (%), molecular weight (KDa), GO description and SecretomeP and ApoplastP outputs ar...

Overview of the protein groups detected peptides overlapping with NP24 and PR-5x. Filled in green the LFQ intensities obtained by only using unique peptides for the protein quantification. LFQ intensities are represented in Log10 scale.

Tomato proteins identified and label-free quantified in Bioassay 1. Samples labeled as ‘Mock’ for the water control, and ‘Endo,’ ‘Coinoc’ and ‘Patho’ for Fo47-inoculated, Fo47:Fol007-coinoculated and Fol007-inoculated C32 susceptible tomato plants. DAPs are marked with +. LFQ values are represented in Log10 scale. Sequence coverage (%), molecular w...

Fusarium oxysporum is an economically important pathogen causing wilting or rotting disease symptoms in a large number of crops. It is proposed to have a structured, “two-speed” genome: i.e. regions containing genes involved in pathogenicity cluster with transposons on separate accessory chromosomes. This is hypothesized to enhance evolvability. Gi...

The fungus Fusarium oxysporum f.sp. cubense (Focub) causes Fusarium wilt of banana. Focub strains are divided into races according to their host specificity, but which virulence factors underlie these interactions is currently unknown. In the F. oxysporum f.sp. lycopersici (Fol)-tomato system, small secreted fungal proteins, called Six proteins, we...

List of primers being used in this study. (DOCX)

PCR control of FocubΔSIX1a and FocubΔSIX1a::SIX1a. In the FocubΔSIX1a strain (KO), the SIX1a ORF has been replaced by a hygromycin resistance cassette. The FocubΔSIX1a::SIX1a strains (C1-7) have regained the gene by transformation. The upper panel shows the presence of the hygromycin resistance cassette both in the knock-out mutant and in the ectop...

Disease scoring system for external and internal symptoms in banana bioassay. (PDF)

Phenotypic visualization of internal symptoms in the FocubΔSIX1a and SIX1a transformants of FocubΔSIX1a. (PDF)

Sequences used in this study. (XLSX)

The plant immune system employs resistance (R) genes to detect the presence of pathogenic microbes by the avirulence (Avr) factors they produce. Whereas some R-genes confer extreme resistance, completely blocking pathogen proliferation, others act later during infection and allow initial microbial multiplication in the host. We hypothesized that tr...

Fusarium oxysporum f. sp. cubense tropic race 4 (Foc TR4) strain which belong to Vegetative Compatibility Group (VCG) 01213 is the most devastating disease in global banana production. Validation of specific primer sets using the positive control (Foc TR4). In total, 50 isolates of Foc are collected from several banana production regions in Indones...

The genome of Fusarium oxysporum (Fo) consists of a set of eleven 'core' chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, an...

The polyphyletic nature of many formae speciales of Fusarium oxysporum prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in t...

Background The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results A total of 61 complete mitogenom...

The mimp family of miniature inverted-repeat transposable elements was previously found only in genomes of Fusarium oxysporum and is contextually associated with virulence genes in this species. Through extensive comparative analysis of 83 F. oxysporum and 52 other Fusarium genomes, we uncovered the distribution of different mimp families throughou...

Many fungi can live both saprophytically and as endophyte or pathogen inside a living plant. In both environments, complex organic polymers are used as sources of nutrients. Propagation inside a living host also requires the ability to respond to immune responses of the host. We review current knowledge of how plant-pathogenic fungi do this. First,...

Plants actively perceive and respond to perturbations in their cell walls which arise during growth, biotic and abiotic stresses. However, few components involved in plant cell wall integrity sensing have been described to date. Using a reverse-genetic approach, we identified the Arabidopsis thaliana leucine-rich repeat receptor kinase MIK2 as an i...

The role of MIK2-LIKE in responses triggered by cellulose biosynthesis inhibition and control of root growth angle. (A) Phylogenetic tree based on homology in the C-terminal domain of MIK2 proteins in Arabidopsis thaliana (A.t.), Arabidopsis lyrata (A.l.) and Brassica rapa (B.r.). Regions homologous to Arabidopsis thaliana MIK2 amino acids 620–1045...

ISX-induced CESA3 internalization in mik2-1 and the1-1 mutant background. (A,B) Confocal images of GFP-CESA3 in cesa3je5, cesa3je5 mik2-1, or cesa3je5 the1-1 genetic background. Four-day-old Arabidopsis seedlings were mock treated or treated with 0.1 μM ISX for 2 h. Panel A displays the cell surface, while panel B displays a cross section through t...

Mik2 and the1 have distinct effects on cell wall structure in the root tip. (A) Quantification of the orientation of cellulose microfibrils relative to the direction of cell elongation in root tips of 7-day-old Arabidopsis seedlings. Values of 3 independent experiments were combined. Error bars represent standard error of n = 10 roots. (B,C) FT-IR...

The role of atlure receptor complex components in response to cellulose biosynthesis inhibition and control of root growth angle. (A) Immune marker gene expression in 13-day-old Arabidopsis seedlings determined by qRT-PCR. Seedlings were mock treated, or treated with 0.6 μM ISX for 9 h. Expression of the immune marker gene CYP81F2 was normalized re...

MIK2, MIK2-LIKE and THE1 expression in different organs. Expression of MIK2, MIK2-LIKE, and THE1 in different organs [80]. (TIF)

MIK2 is not required for hypocotyl growth reduction in prc1-1 genetic background. Five-day-old seedlings grown in an upright position in the dark on MS agar medium supplemented with 1% sucrose. Hypocotyl length was quantified. Error bars represent standard error of n = 18 biological replicas. Different letters indicate statistically significant dif...

Biochemical analysis of cell wall composition in Col-0, mik2-1, the1-1, and mik2-1 the1-1 plants. Levels of cellulose, pectin (galacturonic acid (GA)), and monosaccharides derived from hemi-cellulose or pectin, in roots of 7-day-old Arabidopsis seedlings. Values are expressed per mg root tissue. Depicted is the average of four independent experimen...