Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom‐2 resistance gene in melon

Schmidt, Sarah M.; Lukasiewicz, Joanna; Farrer, Rhys A.; Dam, Peter van; Bertoldo, C.; Rep, Martijn

doi:10.1111/nph.13584

Cited by 84 publications

(108 citation statements)

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“…RNA-Seq, ESTs/cDNAs) examining the F. oxysporum -host interaction have been reported, including those from infected roots of Arabidopsis , cabbage, banana, melon, cotton, chickpea, soybean or Medicago . The majority of these studies only included comparative analyses amongst plant transcripts due to insufficient sequencing depth for fungal transcript detection [19, 31, 48, 50–59]. Transcriptome analysis of this pathogen is also hindered by inherent variations in F. oxysporum root-colonisation dynamics at early stages of host colonisation and subsequent variations in disease progression amongst individual plants.…”

Section: Discussionmentioning

confidence: 99%

“…Those studies with probes unique to the pathogen or enough coverage to detect pathogen transcripts are limited and have typically involved analysis of later time-points in the pathogen-host interaction process. For example, Schmidt and colleagues [48] analysed the expression of F. oxysporum f. sp. melonis transcripts at 10 dpi on melon roots.…”

Section: Discussionmentioning

confidence: 99%

“…Fom _16301 contains a lysin motif (LysM) and shares some similarity to extracellular protein7 (Ecp7) of unknown function from the tomato fungal pathogen Cladosporium fulvum and a LysM containing effector candidate from F. oxysporum f. sp. melonis [48, 77]. It is suggested that other C. fulvum effectors containing the LysM-domain may suppress chitin triggered immunity by protecting fungal hyphae against host chitinases or sequestering fungal cell wall derived chitin fragments from host detection [77–80].…”

Section: Discussionmentioning

confidence: 99%

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Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

et al. 2016

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BackgroundPathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume Medicago truncatula and a pathogenic F. oxysporum forma specialis (f. sp.) medicaginis (Fom). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession.ResultsHigh coverage RNA-Seq of Fom infected root samples harvested from susceptible (DZA315) or resistant (A17) M. truncatula seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of in planta differentially expressed genes. This included enrichment, particularly in DZA315 in planta up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high in-planta induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other F. oxysporum ff. spp. as well as other Fusaria (F. solani, F. fujikori, F. verticilloides, F. graminearum and F. pseudograminearum), and from another wilt pathogen of the same class, a Verticillium species. Overall, this suggests these novel effector candidates may play important roles in Fusaria and wilt pathogen virulence.ConclusionCombining high coverage in planta RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible M. truncatula host. The knowledge from this first in depth in planta transcriptome sequencing of any F. oxysporum ff. spp. pathogenic on legumes will facilitate the dissection of Fusarium wilt pathogenicity mechanisms on many important legume crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3192-2) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

et al. 2016

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“…Whole-genome sequences of closely related fungal species has provided new insight into many other economically important fungal pathogens (Jones et al 2014;Schmidt et al 2016), including other fusaria (Maphosa et al 2016). This diagnostic tool can easily be expanded in the event that other AFC-Euwallacea mutualists are introduced into the United States.…”

Section: Discussionmentioning

confidence: 99%

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

et al. 2017

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Asian Euwallacea ambrosia beetles vector Fusarium mutualists. The ambrosial fusaria are all members of the ambrosia Fusarium clade (AFC) within the Fusarium solani species complex (FSSC). Several EuwallaceaFusarium mutualists have been introduced into nonnative regions and have caused varying degrees of damage to orchard, landscape, and forest trees. Knowledge of symbiont fidelity is limited by current identification methods, which typically requires analysis of DNA sequence data from beetles and the symbionts cultured from their oral mycangia. Here, polymerase chain reaction (PCR)-based diagnostic tools were developed to identify the six Fusarium symbionts of exotic Euwallacea spp. currently known within the United States. Whole-genome sequences were generated for representatives of six AFC species plus F. ambrosium and aligned to the annotated genome of F. euwallaceae. Taxon-specific primer-annealing sites were identified that rapidly distinguish the AFC species currently within the United States. PCR specificity, reliability, and sensitivity were validated using a panel of 72 Fusarium isolates, including 47 reference cultures. Culture-independent multiplex assays accurately identified two AFC fusaria using DNA isolated from heads of their respective beetle partners. The PCR assays were used to show that Euwallacea validus is exclusively associated with AF-4 throughout its sampled range within eastern North America. The rapid assay supports federal and state agency efforts to monitor spread of these invasive pests and mitigate further introductions.Several destructive fungal plant pathogens vectored by exotic bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) have invaded American landscapes and forests within the past century. For example, the redbay ambrosia beetle Xyleborus glabratus (Eichhoff) and its fungal symbiont Raffaelea lauricola T. C. Harr., Fraedrich & Aghayeva are responsible for the death of hundreds of millions of native Lauraceous plants, including avocado (Persea americana), redbay (P. borbonia), and sassafras (Sassafras albidum) (Fraedrich et al. 2008;Ploetz et al. 2013) throughout the coastal southeastern United States. Another group of scolytine beetles, the exotic Euwallacea ambrosia beetles, pose a threat to landscape trees as well as avocado Kasson et al. 2013;Mendel et al. 2012).At least six Euwallacea spp. from Asia have become established within the United States (Cognato et al. 2015;O'Donnell et al. 2015): Euwallacea interjectus (Blandford), E. validus (Eichhoff), E. denticulus (Motschulsky), and three morphologically cryptic species within the E. fornicatus species complex (Eichhoff) (Atkinson 2016;O'Donnell et al. 2015;Storer et al. 2015). Euwallacea spp. are fungus-farming ambrosia beetles that cultivate mutualistic fungi in the genus Fusarium, although this is presently unconfirmed for E. denticulus. Most of these insect species do not cause noticeable economic or ecological damage and, instead, attack and colonize declining and recently killed trees. Howe...

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“…The genus is divided into several distinct species complexes, each with many species [1]. For example, the Fusarium oxysporum species complex is composed of a variety of species including plant and animal pathogens, decomposers and soil fungi [2–5]. The genomes of at least ten F. oxysporum isolates were sequenced in an attempt to delineate the genetic basis of niche specialization, and lineage specific regions within the genome were demonstrated to be important for pathogenicity in plants.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

et al. 2016

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BackgroundThe Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies.ResultsA comparison of genome structure and gene content revealed a 93–99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection.ConclusionsThe genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3371-1) contains supplementary material, which is available to authorized users.

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Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom‐2 resistance gene in melon

Cited by 84 publications

References 60 publications

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

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