Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits
Bibliographic record
Abstract
Protein disulfide isomerase (PDI) is an important enzyme for protein folding in endoplasmic reticulum. The PDI gene family has been systematically studied in Arabidopsis, barley, rice, and bread wheat; however, little is known about this gene family and their roles during fruit development and ripening in fruit trees. In this study, 63 PDI genes were isolated from 8 fruit trees. Phylogenetic trees showed that these genes were clustered into six different groups, designated as A to F. In the groups, the PDI genes had significant differences in gene structure and conserved regions. The chromosome location of each PDI gene was determined in complete genome-assembly fruit trees and the synteny of chromosome segments was detected among peach, pear, and strawberry. Expression profiles of PDI genes in peach, pear, and strawberry showed that nearly all genes in group D and E were more highly expressed in developmental and ripening fruit tissues than those in other groups, while all genes in group A and B presented the lowest levels of expression in fruits of each stage. Moreover, qRT-PCR analyses revealed that these expressed genes were stable expressed in pear and peach fruits, as well as the reported reference genes. Eventually, PbPDI.F1 presented the highest expression stability in pear fruit while PpPDI.F displayed stronger stability than other genes in peach fruit. Thus, these two genes, which were clustered in group F, are good reference genes for gene expression studies during fruit development and ripening.
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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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".