Phylogenetic relationships among the first and second introns of selected <i>Prunus S</i>-RNase genes
Bibliographic record
Abstract
Rahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145–1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap.
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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 | 0.001 | 0.001 |
| 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 | 0.001 |
| 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".