The Genome Sequence of Five Genotypes of<i>Fusarium oxysporum</i>f. sp.<i>vasinfectum</i>: A Resource for Studies on Fusarium Wilt of Cotton

Seo, Seungyeon; Pokhrel, Ambika; Coleman, Jeffrey J.

doi:10.1094/mpmi-07-19-0197-a

Cited by 19 publications

(15 citation statements)

References 18 publications

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“…The trimmed reads from samples of Fov ‐infected Fov7 _KO#5 hypocotyls and in vitro‐grown Fov were mapped to the genome of Fov race 4. [ 28 ] It was found that 0.08–0.68% of the total reads derived from Fov at 5–10 dpi, yielding uniquely aligned read counts from 20799 to 236807 (Table S6, Supporting Information). The varied fungal mRNA reads over the time course revealed hyphal proliferation within host xylem vessels.…”

Section: Resultsmentioning

confidence: 99%

“…Raw reads were trimmed by fastp to get clean reads. [ 73 ] The trimmed reads of J668 and Fov7 _KO#5 were uniquely mapped to the TM‐1 genome [ 74 ] with HISAT2 [ 75 ] using the –dta option, the trimmed reads of Fov7 _KO#5 were also uniquely mapped to the Fov race 4 genome [ 28 ] with Fov spores cultured in vitro as control. Since lacking of gene prediction and annotation of Fov race 4 genome, MAKER pipeline [ 76 ] was used to predict protein‐coding genes of Fov race 4, protein domains and Gene Ontology (GO) terms for each gene were annotated using InterProScan.…”

Section: Methodsmentioning

confidence: 99%

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A Single‐Nucleotide Mutation in a GLUTAMATE RECEPTOR‐LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

et al. 2021

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Fusarium wilt (FW) disease of cotton, caused by the fungus Fusarium oxysporum f. sp. vasinfectum (Fov), causes severe losses in cotton production worldwide. Though significant advancements have been made in development of FW‐resistant Upland cotton (Gossypium hirsutum) in resistance screening programs, the precise resistance genes and the corresponding molecular mechanisms for resistance to Fov remain unclear. Herein it is reported that Fov7, a gene unlike canonical plant disease‐resistance (R) genes, putatively encoding a GLUTAMATE RECEPTOR‐LIKE (GLR) protein, confers resistance to Fov race 7 in Upland cotton. A single nucleotide polymorphism (SNP) (C/A) in GhGLR4.8, resulting in an amino acid change (L/I), is associated with Fov resistance. A PCR‐based DNA marker (GhGLR4.8SNP(A/C)) is developed and shown to cosegregate with the Fov resistance. CRISPR/Cas9‐mediated knockout of Fov7 results in cotton lines extremely susceptible to Fov race 7 with a loss of the ability to induce calcium influx in response to total secreted proteins (SEPs) of Fov. Furthermore, coinfiltration of SEPs with GhGLR4.8A results in a hypersensitive response. This first report of a GLR‐encoding gene that functions as an R gene provides a new insight into plant–pathogen interactions and a new handle to develop cotton cultivars with resistance to Fov race 7.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A Single‐Nucleotide Mutation in a GLUTAMATE RECEPTOR‐LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

et al. 2021

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“…Plant pathogenic fusaria have been assessed for interspecific genetic variation to identify genomic features important for plant host infection [ 1 , 2 ]. In addition, intraspecific genetic variation is a powerful tool to identify potential mechanisms for disease development by pathogenic fungi [ 31 , 32 ]. This study presents a whole genome comparison between two F. oxysporum isolates collected from koa roots, one pathogenic ( Fo koae 44) and one non-pathogenic ( Fo 170) isolates.…”

Section: Discussionmentioning

confidence: 99%

Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

et al. 2020

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Background Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. Results This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. Conclusions These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.

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“…We downloaded 490 nucleotide assemblies of FOSC publicly available on GenBank (including genomes from these studies: Ma et al 2010 , Thatcher et al 2012 , Guo et al 2014 , Kitts et al 2016 , Pu et al 2016 , van Dam et al 2016 , Williams et al 2016 , Singh et al 2017 , van Dam & Rep 2017 , Armitage et al 2018 , Ayhan et al 2018 , Lv et al 2018 , Urbaniak et al 2018 , Asai et al 2019 , Gebru et al 2019 , Henry et al 2019 , Seo et al 2019 , Taylor et al 2019 , Urbaniak et al 2019 , Achari et al 2020 , Batson et al 2020 , Fokkens et al 2020 , Henry et al 2020 , Hudson et al 2020 , Kanapin et al 2020 , Khayi et al 2020 , Kim et al 2020 , Krasnov et al 2020 , Li et al 2020 , Srivastava et al 2020 , Thangavelu et al 2020 , Wang et al 2020 , Yu et al 2020 , Zhang et al 2020 , Henry et al 2021 , Chang & Cook unpublished). Genes were predicted in Augustus using a model of F. graminearum ( Stanke & Morgenstern 2005 ).…”

Section: Methodsmentioning

confidence: 99%

Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

McTaggart

James

Shivas

et al. 2021

Studies in Mycology

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The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.

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The Genome Sequence of Five Genotypes ofFusarium oxysporumf. sp.vasinfectum: A Resource for Studies on Fusarium Wilt of Cotton

Cited by 19 publications

References 18 publications

A Single‐Nucleotide Mutation in a GLUTAMATE RECEPTOR‐LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

A Single‐Nucleotide Mutation in a GLUTAMATE RECEPTOR‐LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex

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