Deciphering the complete plastid genome of an endemic monotypic species <i>Kostermansia malayana</i> (Malvaceae) from Peninsular Malaysia: structural comparative genomics and phylogenomic placement
Bibliographic record
Abstract
Kostermansia malayana Soegeng, a species of Malvaceae endemic to the Malay Peninsula, is threatened by its rare flowering rate and habitat loss due to agriculture land conversion. The species is currently listed as “Vulnerable” on the International Union for Conservation of Nature Red List of Threatened Species. To expand genomic information, the study characterised its plastid genome (plastome) and conducted genome comparative and phylogenetic analyses with other selected species of Malvaceae. The quadripartite-structured plastome was 161 750 bp long and contained 83 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. The overall GC content was 36.3%. Repeat analyses revealed 49 large repeats and 205 simple sequence repeats. A high preference for A/U-ended amino acids was found. Eight and nine PCGs were positively selected when compared to Coelostegia griffithii Benth. & Hook.f. and Reevesia thyrsoidea Lindl., respectively. A notable degree of collinearity was identified between the plastomes of K. malayana and six selected taxa of Helicteroideae. The phylogenetic tree reconstruction based on the concatenated PCG dataset showed a nearly well-resolved relationship within Malvaceae, with K. malayana placed under the Helicteroideae clade. The genomic data will provide a basis for future studies on the genetic conservation, phylogenetics, and evolutionary patterns of Durioneae and Malvaceae.
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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 | 0.001 | 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".