Additional file 2 of Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens
Bibliographic record
Abstract
Additional file 2: Figure S1. SNP frequencies in coding, intronic and intergenic sequences in different U. virens strains relative to UV8b genome. The strains are indicated by different colors. Genomic sequences of these strains were aligned to the reference genome with nucmer, and SNPs were called with “show-snps”, a tool in Mummer package. The genes exhibiting full-length gene sequences in the assemblies of all these strains were subjected to SNP calculation. For each strain, lineage-specific regions were excluded from the intergenic regions to avoid the potential miscalculation. Figure S2. Potential inter-chromosomal translocation events illustrated by alignments of DNA sequences between UV8b and UVP1 genomes. Syntenic alignments are indicated by blue stripes. The inter-chromosomal translocation region is indicated by red box. Alignment analysis between these two genomes was conducted with nucmer. The structure variations were identified with the thresholds of the alignment length of ≥200 bp and the identity of ≥95%. Figure S3. The nucleotide diversities in long terminal repeats (LTRs) at flanking regions of LTR-retrotransposons in SVs, LSRs and other regions of UVP1 genome. The LTRs at both flanking regions of LTR-retrotransposons were aligned to each other and the nucleotide diversities were calculated. LTR-RTs, LTR-retrotransposons. Figure S4. The distribution of the lineage-specific regions (LSRs) of UV8b relative to multiple U. virens strains. The lines from top to bottom indicate the genes (orange), transposable elements (TEs) (blue), heatmap of SNPs compared with multiple strains (red), UV8b-specific LSRs that are absent in all other strains (green), and LSRs compared with the indicated strains (grey). LSRs relative to a specific strain were identified by aligning the sequencing reads of this strain to UV8b genome. For IPU010 and GVT without publicly available sequencing reads, the Illumina reads with 100× coverage were simulated based on their assemblies. The other three chromosomes (2, 3, 6) were displayed in Fig. 4. UV8b-LSR, UV8b-specific LSRs. Figure S5. The phylogenetic relationship among U. virens and the related fungal species based on mitochondrial protein sequences. Homologous mitochondrial protein sequences in these indicated fungal species were aligned using ClustalW, and the tree was constructed using the Neighbor-Joining method in MEGA X with 1000 bootstraps. Figure S6. Certain candidate effector genes are located at the lineage-specific regions of UV8b relative to UVP1. Syntenic alignments are indicated by blue stripes. The effector genes are indicated by red boxes, while other genes are indicated by grey boxes. Alignment analysis was performed as described in Figure S2.
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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 | 0.013 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.001 |
| Bibliometrics | 0.004 | 0.007 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.793 | 0.145 |
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".