Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Musa acuminata
Bibliographic record
Abstract
U-box proteins are a class of E3 ubiquitin ligases structurally similar to RING finger proteins but independent of metal ion coordination, and they play important regulatory roles in various biological processes such as cellular stress responses and protein homeostasis. However, research on U-box genes in banana (Musa acuminata, Cavendish, ‘DH-PaHang’) remains limited. In this study, we identified 90 MaPUBs based on the genome sequence of Musa acuminata. Phylogenetic analysis revealed that PUB genes from Musa acuminata, Arabidopsis thaliana, Oryza sativa and Mangifera indica could be categorized into four distinct groups (I–IV). Additionally, the examination of conserved motifs and gene architectures further validated the phylogenetic tree, offering compelling support for the inferred evolutionary relationships. The MaPUBs are distributed across all 11 chromosomes at varying densities. The analysis of cis-acting elements indicates that MaPUBs are potentially involved in diverse biological processes, reflecting their functional versatility in modulating gene expression and cellular functions Based on transcriptomic data showing distinct expression patterns of MaPUB genes at five time points under drought stress, we randomly selected 12 genes for qRT-PCR analysis to identify drought-tolerance candidates. Based on transcriptomic analysis and expression profiling validation, we selected the MaPUB79 gene, which exhibited high expression levels across all three time periods and was consistent with the RNA-Seq data, for further functional validation to elucidate its role in the drought response mechanism.Using virus-induced gene silencing (VIGS) to suppress MaPUB79 expression led to a marked decline in the drought resistance of Musa acuminata. In summary, this study performed a systematic genome-wide characterization of the PUB gene family in Musa acuminata, offering key insights into PUB-mediated drought resistance mechanisms. These findings provide a theoretical basis for future investigations into the functional roles and underlying mechanisms of the crop’s response to drought stress.
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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) | 0.001 | 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".