Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.
Why this work is in the frame
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Bibliographic record
Abstract
The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 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 it