Improved genome assembly of whale shark, the world’s biggest fish: revealing “chromocline” in intragenomic heterogeneity
Bibliographic record
Abstract
Abstract High-quality chromosome-level assemblies are essential for understanding genome evolution but remain difficult to obtain for large and complex genomes. Here we present a near gap-free genome assembly of the whale shark ( Rhincodon typus ) generated with long-read sequencing and Hi-C scaffolding, markedly improving contiguity and completeness. In particular, the X chromosome was extended to nearly twice its previous length, and putative pseudoautosomal regions were identified. Moreover, we report the first Y-linked scaffolds for this species. Comparative analyses with the zebra shark revealed exceptionally low substitution rates across the genome. We further detected a negative correlation between chromosome length and synonymous substitution rate ( d S ), explained by a positional gradient, designated as “chromocline”, in which substitution rates gradually decrease from chromosomal ends toward central regions. Notably, the X chromosome exhibited low d S compared with autosomes of similar size, consistent with male-driven evolution. Our results highlight positional and sex-chromosome effects as key determinants of molecular evolutionary rates. The improved assembly will enable broad application to population-genetic and conservation genomic analyses in the whale shark.
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How this classification was reachedexpand
Direct model labels (unvalidated)
Per-model category and study-design labels from the labeling rounds. They are machine output, unvalidated, and the disagreement between models ships as data. No study design here is MEDLINE-validated yet.
| Model arm | Categories | Study design | Confidence |
|---|---|---|---|
| gemma | no category Domain: not available · Genre: Empirical About the Canadian research system: no · About a Canadian topic: no | Bench or experimental | low |
| gpt | no category Domain: not available · Genre: Empirical About the Canadian research system: no · About a Canadian topic: no | Bench or experimental | low |
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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| 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, unvalidatedLabeled directly by 2 models reading the full record.
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".