Comparative genomics of <i>Fusarium oxysporum</i> f. sp. <i>melonis</i> strains reveals nine lineages and a new sequence type of <scp>AvrFom2</scp>

Sabahi, Fatemeh; Sain, Mara de; Banihashemi, Z.; Rep, Martijn

doi:10.1111/1462-2920.15339

Cited by 7 publications

(13 citation statements)

References 31 publications

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“…Currently, nine vegetative compatibility groups (VCGs), VCGs 0130–0138, are identified in Fom strains worldwide [ 10 – 12 ]. These VCGs correspond to clonal lines [ 13 ]. Fusarium wilt is difficult to manage because the pathogen can persist in the soil as dormant propagules for decades and can also persist by colonizing crop residue or roots of non-susceptible crops grown in rotation with melon [ 14 ].…”

Section: Objectivementioning

confidence: 99%

“…We carried out whole-genome sequencing of 38 Fusarium oxysporum (Fo) strains which includes three, five, eight, and thirteen strains of races 0, 1, 2, and 1.2, respectively, four strains of which we could not determine the race, and five non-pathogenic strains (Table 1 ). We have already used these data for comparative population genomics to identify putative effector genes and better understand the genetic relationships between the different Fom lineages [ 13 ].…”

Section: Objectivementioning

confidence: 99%

“…In order to obtain insight into the genomic diversity and relationship between clonal linages of Fom, we collected a diverse set of Fom strains originating from different geographical locations across the world including Belgium [ 33 ], China [ 31 , 32 ], France [ 24 , 35 , 36 , 43 ], Iran [ 22 , 23 , 38 – 40 , 42 , 44 , 45 , 48 – 51 , 53 – 59 ], Israel [ 52 ], Japan [ 30 , 41 ], New Zealand [ 28 , 29 ], Spain [ 37 ], the Netherlands [ 26 ], and the United States [ 25 , 34 , 46 , 47 ]. Genomic DNA was isolated as described in Sabahi et al [ 13 ]. The quality of extracted genomic DNA was evaluated by Nano-Drop, Qubit, and agarose gel electrophoresis.…”

Section: Objectivementioning

confidence: 99%

“…Prediction of putative effector genes in Fom genome sequences was carried out by searching uninterrupted ORFs in regions of 2500 bp or 5000 bp downstream of a miniature impala (mimp) terminal inverted repeat (TIR) [ 17 ]. In the present data set, 40 new candidate effector genes were identified [ 13 ]. Phylogenetic analysis of Fom strains was performed by searching for homologues of 440 conserved Fol4287 genes in the sequences of the Fom genomes using megaBLAST with default parameters.…”

Section: Objectivementioning

confidence: 99%

“…We used RaxML v8.2.12 to generate the phylogenetic tree with 100 bootstrap replicates [ 20 ]. According to the presence/absence of candidate effector genes and phylogenetic analyses based on 422 conserved genes, all Fom strains used in our study were grouped in nine genetic lineages [ 13 ]. The presence of highly similar effector patterns between some distant lineages are suggestive of horizontal chromosome transfer between these lineages [ 13 ].…”

Section: Objectivementioning

confidence: 99%

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Genome sequences of 38 Fusarium oxysporum strains

et al. 2022

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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 genetic diversity, population structure and the potential evolutionary trajectories which have led to the emergence of different Fom races, and will facilitate identification of avirulence genes which will be helpful to develop resistant melon cultivars. Data description Genomic DNA was extracted from mycelium of 38 Fusarium oxysporum (Fo) strains collected from different parts of the world including Belgium, China, France, Iran, Israel, Japan, Mexico, New Zealand, Spain, the Netherlands, and the United States. The genomes were sequenced to ≈ 20 × coverage using the Illumina Hiseq Xten system, resulting in paired-end reads of 151 bp and assemblies of 1675 (Fom-18L) to 4472 (Fom-R12-13) scaffolds. The genome sequences are available in the National Center for Biotechnology Information (NCBI) and the Sequence Read Archive (SRA) under Project number PRJNA596396 and PRJNA596396, respectively. The presented data set can be useful to identify the genes associated with pathogenic strategies.

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Section: Objectivementioning

confidence: 99%

Section: Objectivementioning

confidence: 99%

Section: Objectivementioning

confidence: 99%

Section: Objectivementioning

confidence: 99%

Section: Objectivementioning

confidence: 99%

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Genome sequences of 38 Fusarium oxysporum strains

et al. 2022

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Fusarium oxysporum Effector Clustering version 2 (FoEC2): an updated pipeline to infer host range

Guallar¹,

Fokkens

Rep³

et al. 2022

Preprint

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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 their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2.

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Paramyrothecium foliicola causes crown dry rot of melon (Cucumis melo) in Iran

Sabahi

Mirtalebi

Banihashemi

2022

Journal of Phytopathology

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In spring 2018, melon (Cucumis melo L.) plants with wilting of the leaves and dry rot of the crowns were observed in Dashti county, Bushehr province, southern Iran. Nine fungal isolates were recovered from the symptomatic crowns. Based on the morphological characteristics and DNA sequences of the internal transcribed spacer (ITS) region of ribosomal RNA gene, the fungus was identified as Paramyrothecium foliicola L. Lombard and Crous. The pathogenicity of the isolates was confirmed on melon under greenhouse conditions to fulfil the Koch's postulates. Host range determination showed except for pumpkin (Cucurbita moschata L.) and bottle gourd (Lagenaria siceraria L.), several other cucurbit crops exhibited high disease incidence. To our knowledge, this is the first report of crown dry rot of melon caused by P. foliicola in Iran.

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Comparative genomics of Fusarium oxysporum f. sp. melonis strains reveals nine lineages and a new sequence type of AvrFom2

Abstract: Comparative genomics of Fusarium oxysporum f. sp. melonis strains reveals nine lineages and a new sequence type of AvrFom2.

Cited by 7 publications

References 31 publications

Genome sequences of 38 Fusarium oxysporum strains

Genome sequences of 38 Fusarium oxysporum strains

Fusarium oxysporum Effector Clustering version 2 (FoEC2): an updated pipeline to infer host range

Paramyrothecium foliicola causes crown dry rot of melon (Cucumis melo) in Iran

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