Additional file 3 of Genome-wide identification, evolutionary and functional analyses of KFB family members in potato
Bibliographic record
Abstract
Additional file 3 Fig. S1. Gene duplication analysis of potato genome. The local database of potato protein sequences was established by Makeblastdb program. And pairwise comparisons were made between potato protein sequences by Blastp with E-value ≤1e-10. The gene duplication analysis result was obtained by duplicate_gene_classifier program provided in MCScanX software. Singleton: single copy genes; Proximal: adjacent but discontinuous repetitive genes on the same chromosome; Tandem: tandem duplications; WGD or segmental: whole genome duplications or segmental duplications; Dispersed: dispersed genes. Fig. S2. Sequence logos of conserved motifs in StKFB proteins. The 20 conserved motifs of the putative StKFB proteins were identified by MEME software v5.3.0. Fig. S3. The correlation analysis between the expression patterns of StKFBs in diverse potato tissues (a), in potato plants with different treatments (b) and in three colored potato tubers (c). The correlation between the expression levels (FPKM values) of StKFBs was analyzed by Pearson’s correlation coefficient and plotted using the corrplot package v. 0.92 ( https://cran.r-project.org/web/packages/corrplot/ ). Fig. S4. Dissociation curves of primers for qRT-PCR. Dissolution curves were obtained by heating the amplicon from 60 °C (5 s) to 95 °C (50 s) on CFX96 PCR System (Bio-Rad, USA). Fig. S5. Comparison of the expression levels of the 9 selected StKFB genes determined by qRT-PCR and transcriptome sequencing. The boxplots were plotted using tidyverse v. 1.3.1, cowplot v. 1.1.1, ggplot2 v. 3.3.5 and ggsci v. 2.9 packages in RStudio. Values are means ± SD of three replicates in each experiment. Bars with different lowercase letters represent significant difference at p < 0.05. Fig. S6. Conserved domain analysis of StKFB01, AtFKF1, OsFKF1 and StKFB27. The conserved domain analysis was conducted by Conserved Domain Search tool ( https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ) in NCBI.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.966 | 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 teacher head, 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".