Additional file 1 of Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics
Bibliographic record
Abstract
Additional file 1: Figure S1. Physical maps of nucleomorph chromosome 1 for three Cryptomonas species (5 strains in total). Genes on the left indicate transcription from bottom to top, and genes on the right indicate transcription from top to bottom. Colors of the CDS blocks correspond to predicted functional categories, and re-arranged genes are highlighted in yellow. Gene losses between the photosynthetic species C. curvata and the non-photosynthetic species C. paramecium and Cryptomonas sp. CCAC1634B are highlighted in red, and gene losses between C. paramecium and [Crypomonas sp. CCAC1634B and C. curvata] are highlighted in blue. Figure S2. Physical maps of nucleomorph chromosome 2 for three Cryptomonas species. Transcription orientation and color coding is the same as in Figure S1. Figure S3. Physical maps of nucleomorph chromosome 3 for three Cryptomonas species. Transcription orientation and color coding is the same as in Figure S1. Figure S4. Pairwise alignments of amino acids of five putative pseudogenes in C. paramecium CCAP977/2a: sf3b3, sf3b1-like, rarA, cdc5, and nuf2. (a) The red “X” indicates the location of the deletion nucleotide. The translated intergenic sequences between ‘broken’ ORFs are highlighted in yellow. (b) Pairwise alignments of high scoring pairs between the pseudogenes and intact genes. (c) The % amino acid identity and number of amino acid differences between C. paramecium KR and C. curvata KR. Figure S5. Phylogeny of cryptophytes based on nucleomorph small subunit ribosomal RNA gene sequences. The five species whose nucleomorph genomes were compared herein are highlighted red. Cell cartoons show non-photosynthetic (colorless) and photosynthetic (brown-colored) species. The scale bar indicates the inferred number of nucleotide substitutions per site.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.015 |
| 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 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.815 | 0.133 |
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".