Endogenized polinton-like viruses in the dinoflagellate Oxyrrhis marina uncover novel PolB fusion
Bibliographic record
Abstract
Marine viruses are ubiquitous entities that impact the biology of a large fraction of prokaryotic and eukaryotic diversity. Dinoflagellates are heterotrophic, mixotrophic and photosynthetic eukaryotes known for their large and complex nuclear genomes, permanently condensed chromosomes and ability to form toxic algal blooms. We used long-read sequencing to explore the genome of the dinoflagellate Oxyrrhis marina and discovered a novel, endogenized ~25 kbp polinton-like virus (PLV). O. marina PLV (OmPLV) resides primarily in low GC content regions and exhibits a distinctive codon usage pattern, suggesting recent endogenization. OmPLV fragmentation was also observed, suggesting that this element is evolving towards a transposable element-like lifestyle. Notably, OmPLV encodes a unique ~1,500 amino acid fused DNA Helicase SF1–pPolB, representing the largest replication proteins reported so far in Preplasmiviricota. Phylogenetic analysis of the major capsid protein positions OmPLV as a novel PLV lineage related to giant viruses. The discovery of OmPLV provides crucial insight into the evolution and diversification of dsDNA viruses and serves as an important reference point for elucidating the role of endogenized viruses in expansion of dinoflagellate genomes.
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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) | 0.000 | 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, 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".