Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex
Bibliographic record
Abstract
The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi. Comparative genomic study of the Colletotrichum gloeosporioides species complex provides insights into the role of chromosomal rearrangements, mediated by repetitive sequences, drive genetic diversification and host adaptation in the phytopathogens.
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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 | 0.000 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 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".