Understanding plant-pathogen interactions in Septoria tritici blotch infection of cereals

Petit-Houdenot, Y.; Lebrun, M.-H.; Scalliet, Gabriel

doi:10.1201/9781003180715-11

Cited by 4 publications

(5 citation statements)

References 201 publications

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“…Zymoseptoria tritici is an ascomycete fungal pathogen that causes the major wheat foliar disease Septoria tritici blotch (STB). Z. tritici is apoplastic with a biphasic infection process (Petit-Houdenot et al, 2021). After penetration into wheat leaves through stomata, the fungus colonizes the apoplast for 8-3 followed by a rapid onset of necrotic symptoms, associated with the development of fungal asexual fruiting bodies called pycnidia, which contain the pycnidiospores that further spread the disease (Sánchez-Vallet et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…After penetration into wheat leaves through stomata, the fungus colonizes the apoplast for 8-3 followed by a rapid onset of necrotic symptoms, associated with the development of fungal asexual fruiting bodies called pycnidia, which contain the pycnidiospores that further spread the disease (Sánchez-Vallet et al, 2015). STB is currently the economically most important wheat disease in Europe and is mainly controlled using fungicides and genetic resistances (Fones & Gurr, 2015;Petit-Houdenot et al, 2021). However, this disease remains a problem due to the ability of fungal populations to overcome control measures (i.e., fungicide resistance, host resistance breakdown) and adapt to climate changes (Fones & Gurr, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Zymoseptoria tritici is an ascomycete fungal pathogen that causes the major wheat foliar disease Septoria tritici blotch (STB). Z. tritici is apoplastic with a biphasic infection process (Petit-Houdenot et al ., 2021). After penetration into wheat leaves through stomata, the fungus colonizes the apoplast for 8-11 days while the host remains symptomless (Battache et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

“…This long asymptomatic phase is followed by a rapid onset of necrotic symptoms, associated with the development of fungal asexual fruiting bodies called pycnidia, which contain the pycnidiospores that further spread the disease (Sánchez-Vallet et al ., 2015). STB is currently the economically most important wheat disease in Europe and is mainly controlled using fungicides and genetic resistances (Fones & Gurr, 2015; Petit-Houdenot et al ., 2021). However, this disease remains a problem due to the ability of fungal populations to overcome control measures ( i.e ., fungicide resistance, host resistance breakdown) and adapt to climate changes (Fones & Gurr, 2015).…”

Section: Introductionmentioning

confidence: 99%

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A secreted protease-like protein inZymoseptoria triticiis responsible for avirulence onStb9resistance gene in wheat

Amezrou

Audéon

Compain

et al. 2022

Preprint

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Zymoseptoria triticiis the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factorAvrStb9using association mapping and functional validation approaches. PathotypingAvrStb9transgenic strains onStb9cultivars, near isogenic lines and wheat mapping populations, showed thatAvrStb9interacts withStb9resistance gene, triggering a strong immune response.AvrStb9encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector.AvrStb9is also conserved among a globalZ. triticipopulation and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ′atypical′ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Zymoseptoria tritici is an ascomycete fungal pathogen that causes the major wheat foliar disease Septoria tritici blotch (STB). Z. tritici is apoplastic with a biphasic infection process (Petit-Houdenot et al ., 2021). After penetration into wheat leaves through stomata, the fungus colonizes the apoplast for 8-11 days while the host remains symptomless (Battache et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A secreted protease-like protein inZymoseptoria triticiis responsible for avirulence onStb9resistance gene in wheat

Amezrou

Audéon

Compain

et al. 2022

Preprint

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“…The pathogen harbors extensive standing variation from individual infected leaves to large agricultural regions 12,13 . As a consequence, the pathogen showed rapid responses across all major wheat-producing areas to overcome host resistance and gain tolerance to fungicides in less than a decade 10 . Population genomic analyses showed that rapid adaptation of the pathogen was facilitated by parallel evolution across geographic regions 14,15 .…”

mentioning

confidence: 99%

A thousand-genome panel retraces the global spread and climatic adaptation of a major crop pathogen

Feurtey

Lorrain

McDonald

et al. 2022

Preprint

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Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.

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Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

Lapalu

Lamothe

Petit

et al. 2023

Preprint

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Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5' and 3'UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

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Understanding plant-pathogen interactions in Septoria tritici blotch infection of cereals

Cited by 4 publications

References 201 publications

A secreted protease-like protein inZymoseptoria triticiis responsible for avirulence onStb9resistance gene in wheat

A secreted protease-like protein inZymoseptoria triticiis responsible for avirulence onStb9resistance gene in wheat

A thousand-genome panel retraces the global spread and climatic adaptation of a major crop pathogen

Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

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