Identification of effectors with avirulence functions in the pathogenic barley smut fungus, using marker-based approaches and comparison among genomes of related species
Bibliographic record
Abstract
In plant pathology, the molecular genetic analysis of the interaction between pathogen and host yields knowledge applicable to combat crop disease. During infection, pathogens secrete effector proteins to reprogram the host for its benefit. In special cases, recognition of certain effectors by resistance genes, essential components of the host surveillance system, induces resistance to infection. No effectors with such avirulence function have been described for basidiomycete fungi infecting cereals. Ustilago hordei is a biotrophic basidiomycete fungus that infects barley. One of its effectors functions as an avirulence protein, UhAVR1, rendering it avirulent on barley cultivar Hannchen, having corresponding resistance gene Ruh1. I have located UhAvr1 within the genome using a deletion approach and confirmed its resistance-triggering function. I provide evidence that transposable element (TE) activity in the UhAvr1 promoter region and translocation of the coding region are likely responsible for enabling virulence on Hannchen. This region of the genome harbours a cluster of predicted secreted proteins and is syntenic to a cluster in closely-related corn pathogens, U. maydis and Sporisorium reilianum. In U. maydis, deletion of this region results in dramatic reduction in virulence on corn. This region is under selection pressure in both U. maydis and U. hordei likely to avoid recognition by the host. Evolution of the region in U. maydis seems to involve gene duplication and diversification, while in U. hordei this region is saturated with TEs and repeats which can play a role in genome rearrangements. Computational analysis of the U. hordei genome sequence identified 372 candidate secreted effector proteins (CSEPs), many of which are expected to contribute to virulence and some to trigger resistance in analogy to UhAVR1. Most CSEPs are Ustilago-specific proteins of unknown function and without similarities to sequences in public databases. Evidence for accelerated evolution was observed when comparing CSEPs among smut species. More than half of these CSEPs have four or more cysteine residues in characteristic patterns, possibly involved in disulphide bridge formation and protein folding. The study of effectors with avirulence function can reveal resistance genes which can be used for crop breeding programs to obtain disease-resistant cultivars.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".