<i>Populus trichocarpa MONOPTEROS/AUXIN RESPONSE FACTOR5</i>(<i>ARF5</i>) genes: comparative structure, sub-functionalization, and<i>Populus</i>–<i>Arabidopsis</i>microsyntenyThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.
Bibliographic record
Abstract
The genome of Populus (poplar) has been shaped by a whole genome duplication event specific to the salicoid lineage. The MONOPTEROS (MP)/AUXIN RESPONSE FACTOR5 (ARF5) transcription factor plays a key role in auxin-mediated morphogenesis and vascular development in Arabidopsis , and may play a similar role in secondary xylem development in Populus. We used EST and genome sequence information to identify and characterize two duplicated Populus MP genes, PoptrMP1 and PoptrMP2. PoptrMP1 and PoptrMP2 DNA binding and other domains are highly conserved relative to Arabidopsis MP, while the glutamine-rich middle domains are divergent. The two PoptrMP genes are located on duplicated regions of linkage groups II and V. Comparative analysis of the surrounding genes in both the Populus and Arabidopsis genomes revealed a high degree of conservation of gene content and order extending over 11 genes in the immediate vicinity, but also specific changes to genomic regions surrounding each MP locus, providing insights into genome evolution. Expression studies showed that PoptrMP1 and PoptrMP2 have overlapping but distinct expression patterns, suggesting that subfunctionalization of the duplicated genes has occurred, with PoptrMP1 specialized for expression in developing secondary xylem. Transgenic Populus lines overexpressing PoptrMP1 exhibited a 2–4 fold increase in expression of a Populus AtHB8 homolog, a proposed MP target gene, confirming conservation of this regulatory module.
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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) | 0.001 | 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 | 0.001 |
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".