A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogen <i>Claviceps purpurea</i>
Bibliographic record
Abstract
Abstract Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms, which is often governed by variable gene content. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (∼ 38%) that is likely maintained by high recombination rates (ρ = 0.044) and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion is likely controlled by these high recombination rates, which may additionally be influencing the overall trend of purifying selection across the genome. Despite this trend, we observed a strong positive selection pressure on secondary metabolite genes, particularly within the ergoline biosynthetic cluster where we also revealed that the lpsA1 and lpsA2 genes were the result of a recombination event. These results indicate that secondary metabolites are primary factors affecting the diversification of the species into new ecological niches and help maintain its global distribution and broad host range. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism. Author Summary The use of genomic data to better understand the lifestyle of a pathogen and its relationship with its host has expanded our ability to investigate the evolutionary history of these organisms. This in turn has allowed us to decipher and understand the ambiguity surrounding the true nature of the fungal plant pathogen Claviceps purpurea . By combining three different types of broad genomic analyses we identified primary factors affecting the evolution and adaptive potential of this pathogen; particularly a large accessory genome, high recombination rates, and positive selection of genes associated with stress tolerance. These factors likely contribute to the pathogen’s global distribution and broad host range. Furthermore, these findings will influence the direction of future research into optimal control methods.
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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 | 0.000 | 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 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".