Genomic evolution and diversity in Botryosphaeriales: insights from pan-genomic and population genetic analyses of representative species
Bibliographic record
Abstract
Abstract The fungal order Botryosphaeriales includes numerous ecologically and economically important plant-associated taxa, yet its genomic diversity and evolutionary mechanisms remain poorly understood. Here, we present high-quality de novo genome assemblies for three representative species— Botryosphaeria dothidea , Neofusicoccum parvum , and Phyllosticta capitalensis —and perform integrative analyses using comparative genomics, population genetics, and pan-genome frameworks. Pathogenic species ( B. dothidea and N. parvum ) exhibit significant expansions in gene families related to membrane transport and metabolism, suggesting enhanced adaptability and virulence potential. Selective sweep analyses highlight population-level divergence in metabolic and stress-response pathways, reflecting natural selection in host and environmental adaptation. Cross-species pan-genome comparisons of six Phyllosticta species reveal a conserved core genome, dynamic gene family turnover, and extensive horizontal gene transfer from bacterial, and archaeal sources—potentially driving ecological diversification. Furthermore, effector proteins display striking domain variation across genera, particularly in regions associated with host cell wall targeting, indicating convergent strategies for host adaptation. Together, these findings provide comprehensive insights into the genomic evolution, adaptation, and virulence mechanisms of Botryosphaeriales fungi, laying a foundation for future studies on plant–fungal interactions.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".