Phylostratigraphic analysis revealed that ancient ohnologue <i>PtoWRKY53</i> innovated a vascular transcription regulatory network in <i>Populus</i>
Bibliographic record
Abstract
The secondary vascular system represents a hallmark innovation in woody plant evolution. While contemporary studies have decoded key molecular networks governing its development, the evolutionary trajectory of these regulatory systems remains elusive. We performed integrated phylostratigraphic and transcriptomic profiling across six Populus species spanning five phylogenetic clades to decipher the evolutionary dynamics of regulatory genes in the secondary vascular system. This analysis revealed that over 51% of regulatory genes originated from the most ancient phylostratum (PS1). The observed 65% gene expansion in the PS1 was driven by whole-genome duplication (WGD). Through phylotranscriptomic and gene co-expression network analysis, we found that dosage-unconstrained ohnologues from three PS1 families, MYB domain protein, NAC domain containing protein, and WRKY DNA-binding protein, have significant xylem-specific expression. We identified an ohnologue, PtoWRKY53, which forms a new transcription regulatory network in xylem via neofunctionalization. Transgenic analyses revealed that PtoWRKY53 transcriptionally represses PtoCESA3, thereby inhibiting xylem secondary wall biosynthesis and reducing poplar height (26.39%) and stem diameter (18.36%). Our study highlights the importance of interactions between ancient genes and WGD in generating morphological innovations of the secondary vasculature in Populus.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.004 |
| 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 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".