Genomic and transcriptomic analysis of the Whirling disease-resistant Gunnison River Rainbow Trout
Bibliographic record
Abstract
Whirling disease is a debilitating disease of Rainbow Trout caused by Myxobolus cerebralis. The parasite invasion leads to skeletal deformities, neurological impairment, and high mortality. Since its introduction to North America, M. cerebralis has severely impacted wild trout populations in several regions. In this study, we focus on a promising Whirling disease-resistant Rainbow Trout strain developed in the Gunnison River, Colorado. We analyzed the genomes and transcriptomes of this resistant strain at different time points after challenge with M. cerebralis. Signature selection analysis revealed several regions across the genome under selection, with the highest density found on chromosome 23. Several genes found in areas under selection are associated with neuron differentiation and nervous system development. Also, several immuno-genes were under selection, including several with relevance to the innate and adaptive immune response. The transcriptomic analysis revealed that the Gunnison River Rainbow Trout develops a comprehensive immune response after exposure to M. cerebralis. This is supported by the significant enrichment of specific immune response pathways, including differentiation and activation of B-cells and T-cells. These results suggest that certain immune pathways are likely to participate in building the Gunnison River Rainbow Trout's early, mid, and long-term immune response against M. cerebralis, while other pathways related to nervous system development may help juvenile fish survive the effects of Whirling disease. The transcriptomic analysis also reveals that more than half of the top 20 upregulated immune genes are components of the complement pathway. Notably, CD209 (DC-SIGN), a critical gene involved in antigen recognition and dendritic cell function, is among the most highly upregulated genes. The results also indicate the presence of a specific region on chromosome 9 in this strain, previously linked to resistance to this disease. This may explain this strain's strong disease resistance and survival capacity in natural environments.
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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 | 0.000 |
| 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) | 0.001 | 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".