Additional file 1 of Comparing complete organelle genomes of holoparasitic Christisonia kwangtungensis (Orabanchaceae) with its close relatives: how different are they?
Bibliographic record
Abstract
Additional file 1: Figure S1. The plastid genome map of holoparasitic C. kwangtungensis. Genes labelled outside the outer circle are transcribed clockwise, while those inside are transcribed counterclockwise. Dashed area in the inner circle indicates the GC content of plastid genome. Figure S2. Comparison of plastid genome structure among non-parasite (L. philippehsis), hemi-parasite (S. asistica), and holoparasite (C. kwangtungensis). Green lines connect homologous plastid coding genes. Green dotted lines indicate pseudogenized regions. Regions without connecting lines indicate gene loss. Figure S3. The mitochondrial gene map of holoparasitic C. kwangtungensis. Genes labelled outside the outer circle are transcribed clockwise, while those inside are transcribed counterclockwise. Dashed area in the inner circle indicates the GC content of mitochondrial genome. Figure S4. Maximum likelihood phylogeny of rpl20 in the mitochondrial genome of C. kwangtungensis. The phylogenetic tree shows evidence of intracellular gene transfer. The clade length of trees represents the base substitution rate. Figure S5. Gene expression in the photosynthesis pathway observed in transcriptomes of ten species. Detected expressed genes are marked as green. Species in the same clade of C. kwangtungensis are in the red box. With courtesy of © www.genome.jp/kegg/kegg1.html. Figure S6. Gene expression in porphyrin and chlorophyll metabolism pathway observed in the transcriptome of C. kwangtungensis. Genes with detected expression are in the red boxes. The name and number of gene expression products were marked at each node. With courtesy of © www.genome.jp/kegg/kegg1.html. Figure S7. Mitochondrial gene content (core genes in blue and variable genes in yellow) of 21 species including C. kwangtungensis and A. indica. Retained genes are marked in white and lost genes are marked in black. Figure S8. Maximum likelihood phylogenetic tree of Orobanchaceae based on concatenated sequences of all coding genes present in the plastid genome of Lindenbergia philippensis. Table S1. Statistics of putative plastid transferred genes in mitochondrial genome of C. kwangtungensis. Potential donors, transfer types, fragment lengths, and bootstrap of all the putative plastid transferred genes on mitochondrial gnome of C. kwangtungensis. Table S2. Comparison of informative characters of the horizontally transferred fragment rpl20 of C. kwangtungensis and its related species. Table S3. Mitochondrial genome sequence of Lamiales used in this study. Table S4. Plastid genome sequence for plastid phylogeny used in this study.
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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 | 0.002 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.830 | 0.160 |
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".