Poplar defense against insects: genome analysis, full‐length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz‐type protease inhibitor family
Why this work is in the frame
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Bibliographic record
Abstract
*Kunitz protease inhibitors (KPIs) feature prominently in poplar defense responses against insects. The increasing availability of genomics resources enabled a comprehensive analysis of the poplar (p)KPI family. *Using genome analysis, expressed sequence tag (EST) mining and full-length (FL)cDNA cloning we established an inventory and phylogeny of pKPIs. Microarray and real-time PCR analyses were used to profile pKPI gene expression following real or simulated insect attack. Proteomics of insect midgut content was used to monitor stability of pKPI protein. *We identified 31 pKPIs in the genome and validated gene models by EST mining and cloning of 41 unique FLcDNAs. Genome organization of the pKPI family, with six poplar-specific subfamilies, suggests that tandem duplications have played a major role in its expansion. pKPIs are expressed throughout the plant and many are strongly induced by insect attack, although insect-specific signals seem initially to suppress the tree pKPI response. We found substantial peptide coverage for a potentially intact pKPI protein in insect midgut after eating poplar leaves. *These results highlight the complexity of an important defense gene family in poplar with regard to gene family size, differential constitutive and insect-induced gene expression, and resilience of at least one pKPI protein to digestion by herbivores.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 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