Comparative and phylogenetic analyses of 26 Magnoliaceae species based on complete chloroplast genome sequences
Bibliographic record
Abstract
Magnoliaceae is a family of dicotyledonous plants with primitive flowers and is one of the oldest families of flowering plants. In this paper, the chloroplast genomes of 26 species of Magnoliaceae were contrasted and compared to help clarify the relationships among them. The size of the 26 Magnoliaceae chloroplast genomes ranged from 158 177 bp to 160 183 bp, and approximately 1298 simple-sequence repeats were detected. For long-repeat sequences, 197 repeat loci, including 144 forward repeats, 52 palindromic repeats, and 1 reverse repeat, were detected. In four species, an abnormal gene, rpl22, contained premature stop codons. Moreover, three noncoding regions (ccsA-ndhD, ndhD-psaC, and trnH-psbA) with a nucleotide diversity (Pi) value greater than 0.02 and six coding genes (ycf1, petL, matK, psbT, rps19, and ndhF) with a Pi value of no less than 0.008 were identified (this information is important in resolving relationships within the Magnolia genus). The maximum likelihood (ML) and Bayesian inference (BI) trees had the same topological structures, with high support rates among 20 species, i.e., excluding Magnolia dealbata, Magnolia pyramidata, Magnolia dandyi, Magnolia aromatica, Magnolia conifera, and Magnolia glaucifolia. On the whole, these data represent valuable resources for Magnoliaceae chloroplast genomics and will be useful in future phylogenetic studies.
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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 | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 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".