Molecular domestication and transposon contributions to plant genome evolution
Bibliographic record
Abstract
Despite the ubiquity of transposons in eukaryotic genomes, their evolutionary role remains controversial. The discovery of several domesticated genes has suggested that transposons can gain host functions, and thus contribute to the evolution of their host. Here, I present the results of a genome-wide screen for transposon-derived host genes, which was based on the idea that, once domesticated, the open reading frame of such elements would be maintained, while terminal structures necessary for transposition would be lost. Eight-hundred-and-sixty-three such transposon-dissociated elements were mined from the genome of Arabidopsis thaliana var. Columbia-0, of which less than 10% are associated with expression data. Phylogenetic analysis of Mutator superfamily genes in the genomes of Oryza sativa ssp. japonica (cv Nipponbare) and Arabidopsis, including 121 Mutator-derived transposon-dissociated elements, found that only two gene families are taxonomically widespread. MUSTANG1, a member of one of these families, appears to be under purifying selection. Thus, despite the dearth of taxonomically widespread and/or expressed transposon-dissociated elements, MUSTANG1, as well as three transposon-dissociated elements that may be associated with mutant phenotypes, might be newly discovered transposon-derived host genes.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".