Reduced Nuclear Genomes Maintain High Gene Transcription Levels
Bibliographic record
Abstract
Reductive genome evolution is seen in organisms living in close association with each other, such as in endosymbiosis, symbiosis, and parasitism. The reduced genomes of endosymbionts and parasites often exhibit similar features such as high gene densities and A+T compositional bias. Little is known about how the regulation of gene expression has been affected in organisms with highly compacted genomes. We studied gene transcription patterns in "nucleomorph" genomes, which are relic nuclear genomes of algal endosymbionts found in cryptophytes and chlorarachniophytes. We examined nuclear and nucleomorph gene transcription patterns using RNA-Seq transcriptome and genome mapping analyses in representatives of both lineages. In all four examined genomes, the most highly transcribed nucleomorph gene category was found to be plastid-associated genes. Remarkably, only 0.49-3.37% of the nucleomorph genomes of these organisms did not have any mRNA counterpart in our RNA-Seq data sets, and nucleomorph genes show equal or higher levels of transcription than their counterparts in the nuclear genomes. We hypothesize that elevated levels of nucleomorph gene transcription may serve to counteract the degradation or modification of protein function due to the loss of interacting proteins in the nucleomorph and nucleomorph-associated subcellular compartments.
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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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".