Diversity and evolution of <i>repABC</i> type plasmids in <i>Rhodobacterales</i>
Bibliographic record
Abstract
The repABC operon is the prevalent replication unit of alphaproteobacterial plasmids. Their semi-autonomy is ensured by the essential replicase gene repC as well as the repAB partitioning cassette. While conserved repAB modules are widespread among bacterial plasmids and homologues are even responsible for chromosome partitioning, repC genes are exclusively present in Alphaproteobacteria. RepABC operons contain two strong incompatibility regions, namely a small regulative antisense RNA gene (inc alpha) and a palindromic centromere region (inc beta), which were previously used to classify these replicons. The present survey pursued a complementary strategy essentially following the rationale that all plasmids identified from a single bacterium are per se compatible. We established a novel classification scheme for plasmids based on comprehensive phylogenetic analyses of repC, repA and repB genes. Our case study is focused on the Roseobacter clade (Rhodobacterales), one of the most successful lineages of the marine bacterioplankton. Its global significance was shown in several studies and the interest in these organisms is reflected by more than 40 upcoming genome projects. Based on phylogenetic RepC analyses we identified nine compatibility groups that are expected to stably coexist within the same cell. This prediction is supported by RepA and RepB phylogenies, moreover independent evidence is delivered by the group specificity of highly conserved palindromes (inc beta).
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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 teacher head, 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".