Genome mining reveals the distribution of biosynthetic gene clusters in Alternaria and related fungal taxa within the family Pleosporaceae
Bibliographic record
Abstract
BACKGROUND: The advancement of whole genome sequencing techniques has led to the development of genome mining strategies that enable high-resolution research into fungal secondary metabolite (SM) biosynthesis. Alternaria species are producers of prominent SMs including virulence factors and mycotoxins that affect phytosanitation, food safety, and the economy. Here, we apply genome mining to identify a total of 6,323 biosynthetic gene clusters (BGCs) from 187 genomes: 123 Alternaria and 64 from seven other closely related genera in the family Pleosporaceae. RESULTS: An average of 34 BGCs were detected per genome, with 29 on average for Alternaria genomes. The distribution of different BGC classes (e.g. polyketide synthases, non-ribosomal peptide synthetases) across taxa was investigated. BGCs were grouped into 548 gene cluster families (GCFs) revealing that while individuals within the same species may differ in their toxicological potential, the overall patterns of GCF presence/absence were also generally well correlated with phylogenomic patterns at higher taxonomic levels. Comparative genome analyses revealed that the divergent Alternaria sections Infectoriae and Pseudoalternaria possessed highly unique GCF profiles compared to other Alternaria sections, providing nine ideal candidates for diagnostic or chemotaxonomic marker development. However, none of these GCFs were associated with known compounds, prompting further research into the genetic characterization of Alternaria SMs. The GCF for the most prominent Alternaria mycotoxin alternariol (AOH) was found in Alternaria sections Alternaria and Porri, suggesting that food safety monitoring efforts should prioritize these two sections. Findings supported phytosanitary regulations regarding Alternaria gaisen, associated with Asian pear host-specific AK-toxin I. CONCLUSIONS: Our analyses are of unprecedented scale and resolution, allowing the identification of SM BGCs that are shared among multiple genera, or restricted to certain groups of focal taxa. Our study highlights the challenges associated with exploratory genome mining as a launching point for further research, and informs Alternaria disease management and regulation, food safety practices, and natural product discovery.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| 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) | 0.001 | 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".