Comparative and phylogenetic analysis of <i>Platycarya longipes</i> and related species based on the complete chloroplast genomes
Bibliographic record
Abstract
Platycarya longipes is a dominant tree species in karst forests. Due to limited genomic information, its exact phylogenetic position within the family Juglandaceae remains unclear. In this study, the complete chloroplast genome (cp genome) of Platycarya longipes was de novo assembled using Illumina reads. This circular cp genome was 158 592 bp in length, consisting of an 88 066 bp large single-copy region, an 18 524 bp small single-copy region, and a total of 26 001 bp derived from a pair of inverted repeats (IRa and IRb), with an average GC content of 36.15%. It accommodated a total of 113 genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Additionally, within the genome, 49 long repeats and 66 simple sequence repeats, which could be utilized as molecular markers, were identified. In comparison to the related Platycarya strobilacea, the Ka/Ks substitution rate values of Platycarya longipes exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the Platycarya longipes cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between Platycarya longipes and Platycarya strobilacea.
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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".