The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of <i>Garcinia paucinervis</i>
Bibliographic record
Abstract
Garcinia paucinervis is an evergreen tree with high medicinal value. Due to its vulnerable reproductive capacity coupled with excessive logging by humans, G. paucinervis has become an endangered species. In order to protect this species effectively, we drew the complete chloroplast genome of G. paucinervis and performed a series of comparative analyses on G. paucinervis and its neighbouring species. The chloroplast genome size of G. paucinervis is 157702 bp. In the chloroplast genome, we identified 130 genes, 56 RNA editing sites in the protein-coding genes, as well as 241 simple sequence repeats (SSRs) and 49 complex repetitive sequences. Comparative analysis identified some high divergent sequences in the intergenic spacers, which can be used as candidate markers for phylogenetic study. From an adaptive evolution point of view, a branch-site model analysis identified positively selected sites in 5 genes, most of which are involved in ribosome biogenesis, protein synthesis and other developmental processes. The detected codon substitutions may be associated with the evolution of G. paucinervis to adapt to the extreme habitat in karst. In addition, the result of the phylogenetic analysis supports the previous phylogenomic studies of taxa within the rosids clade. The ML tree revealed that G. mangostana was a sister to G. gummi-gutta, and they formed a diverging lineage to G. paucinervis in Garcinia. The above information is of great significance for us to understand the evolution of G. paucinervis chloroplast and lays the foundations for future studies in species conservation.
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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) | 0.002 | 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".