Insights on macrosynteny, ′rebel′ genes, and a new sex-linked region in anurans from comparative genomics and a new chromosome-level genome for the western chorus frog
Bibliographic record
Abstract
Amphibians have unique genome characteristics including slow karyotypic evolution and cytogenetically undifferentiated sex chromosomes. Yet our understanding of amphibian genomes has not kept pace with that of mammals and birds, partially due to scarce genomic resources and challenges associated with large genome sizes and high repetitiveness. We assembled and annotated a chromosome-level genome for the western chorus frog ( Pseudacris triseriata ), a species of conservation concern and importance in evolutionary research. Comparison of our new genome with other chromosome-level frog genomes reveals exceptionally conserved evolution of 13 chromosomal elements and gene orders across over 200 million years of anuran evolution. We uncovered ′rebel′ Benchmarking Universal Single-Copy Orthologs (BUSCO) genes that have been duplicated in almost all frog species, have been transposed, and showed lineage-specific synteny patterns – possibly relating to key traits such as frog advertisement calls and mitochondrial genome evolution. We also assembled a complete mitochondrial genome and found heteroplasmy of both point polymorphisms and length variation in the tandem repeat arrays in the control region. Double-digest restriction-site associated DNA sequencing analysis indicates that the western chorus frog has an XY sex system and the sex-linked region involved an ~1Mb indel structural variant. Overall, our study provides important genomic resources for treefrogs and other anurans, documents highly conserved chromosomal evolution and gene orders in anurans, identifies ′rebel′ genes that might be important for frog evolution, and reveals a new sex-linked region with indel structural variants in anurans.
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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 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| 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) | 0.002 | 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".