Pangenomic analysis reveals pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

AbstractA reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage.Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core.RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.

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Evaluation of antifungal activity of sodium salts against onion basal rot caused by Fusarium oxysporum f.sp. cepae

Plant Protection Science ◽

10.17221/9/2013-pps ◽

2014 ◽

Vol 50 (No. 1) ◽

pp. 19-25 ◽

Cited By ~ 15

Author(s):

M. Türkkan ◽

I. Erper

Keyword(s):

Fusarium Oxysporum ◽

Sodium Fluoride ◽

Mycelial Growth ◽

Sodium Phosphate ◽

Sodium Metabisulfite ◽

Sodium Salts ◽

Minimum Fungicidal Concentration ◽

Basal Rot ◽

Onion Basal Rot

The efficacy of twelve sodium salts as possible alternatives to synthetic fungicides for the control of onion basal rot caused by Fusarium oxysporum f.sp. cepae was evaluated. In vitro tests showed that there were significant differences between the inhibitory effects of sodium salts on the mycelial growth (P ≤ 0.05) and 2% (w/v) concentrations of sodium metabisulfite and sodium fluoride completely inhibited mycelial growth of the fungus, while other salts did not. Sodium metabisulfite and sodium phosphate monobasic had lower pH values than the other salts. Unlike sodium metabisulfite, sodium phosphate monobasic could not decrease the mycelial growth. The ED<sub>50</sub>, minimum inhibition concentration (MIC), and minimum fungicidal concentration (MFC) values indicated that sodium metabisulfite was more inhibitory to the fungus compared to sodium fluoride. In soil tests, inhibitory effect of sodium metabisulfite on the fungus was higher than that of sodium fluoride, where sodium metabisulfite completely inhibited mycelial growth at even 0.4% concentration.

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Molecular characterization of Zn(II)2Cys6 cluster gene family and their association with pathogenicity of the onion basal rot pathogen, Fusarium oxysporum f. sp. cepae

Physiological and Molecular Plant Pathology ◽

10.1016/j.pmpp.2021.101782 ◽

2021 ◽

pp. 101782

Author(s):

Bijayalaxmi Mahanty ◽

Rukmini Mishra ◽

Raj Kumar Joshi

Keyword(s):

Gene Family ◽

Fusarium Oxysporum ◽

Molecular Characterization ◽

Basal Rot ◽

Onion Basal Rot ◽

Cluster Gene

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Draft Genome Sequence of an Onion Basal Rot Isolate of Fusarium proliferatum

Microbiology Resource Announcements ◽

10.1128/mra.01385-18 ◽

2019 ◽

Vol 8 (1) ◽

Cited By ~ 1

Author(s):

Andrew D. Armitage ◽

Andrew Taylor ◽

Michelle T. Hulin ◽

Alison C. Jackson ◽

Richard J. Harrison ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Secondary Metabolite ◽

Genome Sequence ◽

Draft Genome ◽

Fusarium Proliferatum ◽

Draft Genome Sequence ◽

Content Type ◽

Basal Rot ◽

Rot Disease ◽

Onion Basal Rot

Fusarium proliferatum is a component of the onion basal rot disease complex. We present an annotated F. proliferatum draft genome sequence, totaling 45.8 Mb in size, assembled into 597 contigs, with a predicted 15,418 genes. The genome contains 58 secondary metabolite clusters and homologs of the Fusarium oxysporum effector SIX2.

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Survey on Onion Basal Rot Disease Incidence and Evaluation of Aggregatum Onion (Allium cepa L. Var. Aggregatum Don.) Genotypes Against Fusarium oxysporum f. sp. Cepae

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2020.907.058 ◽

2020 ◽

Vol 9 (7) ◽

pp. 529-536

Author(s):

J. Shamyuktha ◽

J. Sheela ◽

N. Rajinimala ◽

B. M. Jeberlinprabina ◽

C. Ravindran

Keyword(s):

Fusarium Oxysporum ◽

Allium Cepa ◽

Disease Incidence ◽

Basal Rot ◽

Allium Cepa L ◽

Rot Disease ◽

Onion Basal Rot

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Control of Fusarium oxysporum f.sp. narcissi, the cause of narcissus basal rot, with thiabendazole and other fungicides

Crop Protection ◽

10.1016/0261-2194(96)00023-3 ◽

1996 ◽

Vol 15 (6) ◽

pp. 549-558 ◽

Cited By ~ 5

Author(s):

G.R. Hanks

Keyword(s):

Fusarium Oxysporum ◽

Basal Rot

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Peer Review #1 of "RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers (v0.1)"

10.7287/peerj.3631v0.1/reviews/1 ◽

2017 ◽

Author(s):

B Davis-Dusenbery

Keyword(s):

Gene Expression ◽

Peer Review ◽

Reference Genes ◽

Rna Seq ◽

Skin Cancers ◽

Expression Studies ◽

Gene Expression Studies ◽

Melanoma Skin

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Identification and quantification of Fusarium oxysporum in planta and soil by means of an improved specific and quantitative PCR assay

Applied Soil Ecology ◽

10.1016/j.apsoil.2010.10.001 ◽

2010 ◽

Vol 46 (3) ◽

pp. 372-382 ◽

Cited By ~ 35

Author(s):

Daniel Jiménez-Fernández ◽

Miguel Montes-Borrego ◽

Juan A. Navas-Cortés ◽

Rafael M. Jiménez-Díaz ◽

Blanca B. Landa

Keyword(s):

Fusarium Oxysporum ◽

Quantitative Pcr ◽

In Planta ◽

Pcr Assay ◽

Quantitative Pcr Assay ◽

Identification And Quantification

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Screening immature bulbs of daffodil (Narcissus L.) crosses for resistance to basal rot disease caused by Fusarium oxysporum f. sp. narcissi

Euphytica ◽

10.1007/bf00024545 ◽

1992 ◽

Vol 63 (3) ◽

pp. 199-206

Author(s):

S. A. Bowes ◽

R. N. Edmondson ◽

C. A. Linfield ◽

F. A. Langton

Keyword(s):

Fusarium Oxysporum ◽

Basal Rot ◽

Rot Disease

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Proline-106 EPSPS Mutation Imparting Glyphosate Resistance in Goosegrass (Eleusine indica) Emerges in South America

Weed Science ◽

10.1017/wsc.2018.71 ◽

2018 ◽

Vol 67 (1) ◽

pp. 48-56 ◽

Cited By ~ 8

Author(s):

Hudson K. Takano ◽

Rafael R. Mendes ◽

Leonardo B. Scoz ◽

Ramiro F. Lopez Ovejero ◽

Jamil Constantin ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Rapid Detection ◽

Resistance Mechanism ◽

Fold Increase ◽

In Planta ◽

Eleusine Indica ◽

Target Site Resistance ◽

Resistance Trait

AbstractGlyphosate-resistant (GR) goosegrass [Eleusine indica(L.) Gaertn.] was recently identified in Brazil, but its resistance mechanism was unknown. This study elucidated the resistance mechanism in this species and developed a molecular marker for rapid detection of this target-site resistance trait. The resistance factor for the resistant biotype was 4.4-fold compared with the glyphosate-susceptible (GS) in greenhouse dose–response experiments. This was accompanied by a similar (4-fold) difference in the levels of in vitro andin plantashikimate accumulation in these biotypes. However, there was no difference in uptake, translocation, or metabolism of glyphosate between the GS and GR biotypes. Moreover, both biotypes showed similar values for 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number and transcription. Sequencing of a 330-bp fragment of theEPSPSgene identified a single-nucleotide polymorphism that led to a Pro-106-Ser amino acid substitution in the enzyme from the GR biotype. This mutation imparted a 3.8-fold increase in the amount of glyphosate required to inhibit 50% of EPSPS activity, confirming the role of this amino acid substitution in resistance to glyphosate. A quantitative PCR–based genotyping assay was developed for the rapid detection of resistant plants containing this Pro-106-Ser mutation.

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