Comparative Analysis of Bacterial-Origin Genes for Plant Mitochondrial Ribosomal Proteins
Bibliographic record
Abstract
Mitochondrial ribosomes contain bacterial-type proteins reflecting their endosymbiotic heritage, and a subset of these genes is retained within the mitochondrion in land plants. Variation in gene location is observed, however, because migration to the nucleus is still an ongoing evolutionary process in plants. To gain insights into adaptation events related to successful gene transfer, we have compiled data for bacterial-origin mitochondrial-type ribosomal protein genes from the completely sequenced Arabidopsis and rice genomes. Approximately 75% of such nuclear-located genes encode amino-terminal extensions relative to their Escherichia coli counterparts, and of that set, only about 30% have introns at (or near) the junction in support of an exon shuffling-type recruitment of upstream expression/targeting signals. We find that genes that were transferred to the nucleus early in eukaryotic evolution have, on average, about twofold higher density of introns within the core ribosomal protein sequences than do those that moved to the nucleus more recently. About 20% of such introns are at positions identical to those in human orthologs, consistent with their ancestral presence. Plant mitochondrial-type ribosomal protein genes have dispersed chromosomal locations in the nucleus, and about 20% of them are present in multiple unlinked copies. This study provides new insights into the evolutionary history of endosymbiotic bacterial-type genes that have been transferred from the mitochondrion to the nucleus.
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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 | 0.001 | 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) | 0.001 | 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".