The 2023 update of target site mutations associated with resistance to fungicides and a web-tool to assist label designations

Oliver, Richard; Hane, James; Mair, Wesley; Lopez-Ruiz, Fran

doi:10.1007/s41348-024-00872-7

Cited by 5 publications

(10 citation statements)

References 55 publications

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“…Although testing of differential fungicide efficacy and resistance across S. pistaciarum isolates was beyond the scope of this current study, it was possible to predict potential fungicide resistance mutations from pan-genomic data. Analysis of amino acid changes in the products of known fungicide resistance loci ( Mair et al, 2016 ) revealed several potential resistance adaptations, inferred from reported resistance associated with equivalent mutations in other fungal species ( Supplementary Data Sheet 6 ; Oliver et al, 2024 ). The CYP51A protein of all isolates contained amino acid residues corresponding to P216L, M220I, and H147Y of Aspergillus fumigatus CYP51A [NCBI: AF338659], which may confer azole resistance ( Howard et al, 2009 ).…”

Section: Resultsmentioning

confidence: 99%

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Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece

Zambounis,

Boutsika,

Gray

et al. 2024

Front. Microbiol.

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Septoria pistaciarum, a causal agent of Septoria leaf spot disease of pistachio, is a fungal pathogen that causes substantial losses in the cultivation, worldwide. This study describes the first pan-genome-based survey of this phytopathogen—comprising a total of 27 isolates, with 9 isolates each from 3 regional units of Greece (Pieria, Larissa and Fthiotida). The reference isolate (SPF8) assembled into a total of 43.1 Mb, with 38.6% contained within AT-rich regions of approximately 37.5% G:C. The genomes of the 27 isolates exhibited on average 42% gene-coding and 20% repetitive regions. The genomes of isolates from the southern Fthiotida region appeared to more diverged from each other than the other regions based on SNP-derived trees, and also contained isolates similar to both the Pieria and Larissa regions. In contrast, isolates of the Pieria and Larissa were less diverse and distinct from one another. Asexual reproduction appeared to be typical, with no MAT1-2 locus detected in any isolate. Genome-based prediction of infection mode indicated hemibiotrophic and saprotrophic adaptations, consistent with its long latent phase. Gene prediction and orthology clustering generated a pan-genome-wide gene set of 21,174 loci. A total of 59 ortholog groups were predicted to contain candidate effector proteins, with 36 (61%) of these either having homologs to known effectors from other species or could be assigned predicted functions from matches to conserved domains. Overall, effector prediction suggests that S. pistaciarum employs a combination of defensive effectors with roles in suppression of host defenses, and offensive effectors with a range of cytotoxic activities. Some effector-like ortholog groups presented as divergent versions of the same protein, suggesting region-specific adaptations may have occurred. These findings provide insights and future research directions in uncovering the pathogenesis and population dynamics of S. pistaciarum toward the efficient management of Septoria leaf spot of pistachio.

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Section: Resultsmentioning

confidence: 99%

“…Secondary metabolite synthesis gene clusters were predicted in the reference isolate assembly (SPF8) with antiSMASH v6.1.1 ( Blin et al, 2021 ). Fungicide-resistance mutations were predicted with the fungicide-resistance allele screening tool (FRAST) ( Oliver et al, 2024 ).…”

Section: Methodsmentioning

confidence: 99%

Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece

Zambounis,

Boutsika,

Gray

et al. 2024

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Secondary metabolite synthesis gene clusters were predicted in the reference isolate assembly (SPF8) with antiSMASH v6.1.1 (Blin et al, 2021). Fungicide-resistance mutations were predicted with the fungicide-resistance allele screening tool (FRAST) (Oliver et al, 2024).…”

Section: Prediction Of Genomic Repeats Genes and Functionsmentioning

confidence: 99%

“…Although testing of differential fungicide efficacy and resistance across S. pistaciarum isolates was beyond the scope of this current study, it was possible to predict potential fungicide resistance mutations from pan-genomic data. Analysis of amino acid changes in the products of known fungicide resistance loci (Mair et al, 2016) revealed several potential resistance adaptations, inferred from reported resistance associated with equivalent mutations in other fungal species (Supplementary Data Sheet 6; Oliver et al, 2024). The CYP51A protein of all isolates contained amino acid residues corresponding to P216L, M220I, and H147Y of Aspergillus fumigatus CYP51A [NCBI: AF338659], which may confer azole resistance (Howard et al, 2009).…”

Section: Potential Fungicide Resistancementioning

confidence: 99%

Data_Sheet_6.XLSX

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“…Secondary metabolite synthesis gene clusters were predicted in the reference isolate assembly (SPF8) with antiSMASH v6.1.1 (Blin et al, 2021). Fungicide-resistance mutations were predicted with the fungicide-resistance allele screening tool (FRAST) (Oliver et al, 2024).…”

Section: Prediction Of Genomic Repeats Genes and Functionsmentioning

confidence: 99%

Data_Sheet_4.XLSX

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The 2023 update of target site mutations associated with resistance to fungicides and a web-tool to assist label designations

Cited by 5 publications

References 55 publications

Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece

Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece

Data_Sheet_6.XLSX

Data_Sheet_4.XLSX

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