Richard Oliver

The novel avirulence effector AlAvr1 from Ascochyta lentis mediates host cultivar specificity of ascochyta blight in lentil

Publisher: Wiley

Date: 04-03-2022

DOI: 10.1111/MPP.13203

Abstract: Ascochyta lentis is a fungal pathogen that causes ascochyta blight in the important grain legume species lentil, but little is known about the molecular mechanism of disease or host specificity. We employed a map‐based cloning approach using a biparental A . lentis population to clone the gene AlAvr1‐1 that encodes avirulence towards the lentil cultivar PBA Hurricane XT. The mapping population was produced by mating A . lentis isolate P94‐24, which is pathogenic on the cultivar Nipper and avirulent towards Hurricane, and the isolate Al Kewell, which is pathogenic towards Hurricane but not Nipper. Using agroinfiltration, we found that AlAvr1‐1 from the isolate P94‐24 causes necrosis in Hurricane but not in Nipper. The homologous corresponding gene in Al Kewell, AlAvr1‐2 , encodes a protein with amino acid variation at 23 sites and four of these sites have been positively selected in the P94‐24 branch of the phylogeny. Loss of AlAvr1‐1 in a gene knockout experiment produced a P94‐24 mutant strain that is virulent on Hurricane. Deletion of AlAvr1‐2 in Al Kewell led to reduced pathogenicity on Hurricane, suggesting that the gene may contribute to disease in Hurricane. Deletion of AlAvr1‐2 did not affect virulence for Nipper and AlAvr1‐2 is therefore not an avirulence gene for Nipper. We conclude that the hemibiotrophic pathogen A . lentis has an avirulence effector, AlAvr1‐1, that triggers a hypersensitive resistance response in Hurricane. This is the first avirulence gene to be characterized in a legume pathogen from the Pleosporales and may help progress research on other damaging Ascochyta pathogens.

Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence

Publisher: Cold Spring Harbor Laboratory

Date: 16-12-2021

DOI: 10.1101/2021.12.16.472873

Abstract: Plant-pathogenic fungi span erse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, controlling development and virulence in plant pathogenic fungi. Recent research has established regulatory roles for several taxonomically conserved fungal TFs, but the evolution of specific virulence regulators is not well understood. This study sought to explore the representation of TFs across a taxonomically- erse range of fungi, with a focus on plant pathogens. A significant trend was observed among the obligate, host-associated pathogens, which possess a reduced overall TF repertoire, alluding to a lack of pressure for maintaining ersity. A novel orthology-based analysis is then presented that refined TF classifications, traditionally based on the nature of the DNA-binding domains. Using this analysis, cases of TF over/underrepresentation across fungal pathogen lineages are systematically highlighted. Specific ex les are then explored and discussed that included the TF orthologues of Ste12, Pf2 and EBR1, plus phytotoxic secondary-metabolite cluster regulators, which all presented novel and distinct evolutionary insights. Ultimately, as the ex les presented demonstrate, this resource can be interrogated to guide functional studies that seek to characterise virulence-specific regulators and shed light on the factors underpinning plant pathogenicity.

Reference Genome Assembly for AustralianAscochyta rabieiIsolate ArME14

Publisher: Oxford University Press (OUP)

Date: 07-2020

DOI: 10.1534/G3.120.401265

Abstract: Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

The identification and deletion of the polyketide synthase‐nonribosomal peptide synthase gene responsible for the production of the phytotoxic triticone A/B in the wheat fungal pathogen

Publisher: Wiley

Date: 21-11-2019

DOI: 10.1111/1462-2920.14854

Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat

Publisher: Public Library of Science (PLoS)

Date: 06-01-2022

DOI: 10.1371/JOURNAL.PPAT.1010149

Abstract: The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1 , respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P . nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in representative P . nodorum isolates from Australia and South Africa. The presence of PE401 removed the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3 . PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P . nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P . nodorum carrying PE401. An infection competition assay between P . nodorum isogenic strains with and without PE401 indicated that the higher Tox1 -expressing strain rescued the reduced virulence of the lower Tox1 -expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both ‘selfish’ and ‘altruistic’ characteristics. This offers an insight into a complex NE-NE interaction that is occurring within the P . nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.

Linkage Projects - Grant ID: LP0346963

Start Date: 08-2003

End Date: 12-2006

Amount: $285,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989071

Start Date: 01-2009

End Date: 07-2012

Amount: $600,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0668536

Start Date: 2006

End Date: 12-2006

Amount: $485,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0987871

Start Date: 2009

End Date: 06-2012

Amount: $242,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0986139

Start Date: 2009

End Date: 12-2011

Amount: $230,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE120100077

Start Date: 01-2012

End Date: 12-2012

Amount: $150,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE140100096

Start Date: 03-2014

End Date: 03-2015

Amount: $180,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0454871

Start Date: 01-2005

End Date: 12-2009

Amount: $399,870.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE110100188

Start Date: 03-2011

End Date: 12-2012

Amount: $550,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0230245

Start Date: 2001

End Date: 12-2002

Amount: $600,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0239218

Start Date: 2001

End Date: 12-2002

Amount: $340,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0560987

Start Date: 03-2005

End Date: 12-2005

Amount: $156,697.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0453722

Start Date: 2004

End Date: 12-2005

Amount: $385,240.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0347922

Start Date: 2002

End Date: 12-2002

Amount: $630,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100029

Start Date: 09-2013

End Date: 12-2016

Amount: $430,138.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0883556

Start Date: 03-2009

End Date: 03-2012

Amount: $76,881.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE120100092

Start Date: 01-2012

End Date: 12-2012

Amount: $240,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE140100036

Start Date: 2014

End Date: 12-2015

Amount: $771,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE150100158

Start Date: 2015

End Date: 12-2015

Amount: $670,000.00

Funder: Australian Research Council