Abstracts of Presentations at IS-MPMI XVIII Congress
Bibliographic record
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease of wheat and barley. The recognition of Pgt as a global threat to food security was substantiated by the emergence of races in the Ug99 lineage from Africa, which are virulent to most wheat cultivars in the world. Similar to other rust fungi, Pgt is a dikaryotic organism, with two haploid nuclei (karyons) during the infection process on wheat. We developed a new strategy to generate haplotype-phased genome assemblies of Pgt using PacBio long reads, to better understand the genomic architecture and evolution of this pathogen. Comparison of a fully haplotype-resolved assembly of Ug99 to two Pgt isolates of the race 21 group found in South Africa and Australia provides evidence that Pgt Ug99 arose by a somatic hybridization event caused by nuclear exchange during the vegetative phase. Inter-isolate comparisons indicated that one complete haplotype of the race 21 isolates is shared with Pgt Ug99. This is S1.2 supported by whole-genome sequence alignments, structural variation analysis, read cross mapping, and phylogenetic analyses. DNA proximity analysis from Hi-C data supports the physical separation of the two predicted haplotypes into separate nuclei. Based on these findings, we propose a model that ascribes the origin of the Pgt Ug99 lineage to a somatic hybridization event that occurred in Africa.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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 teacher head, 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".