Genomic Approaches to Identifying Acylsugar Metabolism Genes in Solanum pennellii
Bibliographic record
Abstract
Acylsugars are specialized metabolites secreted by plants of the nightshade family. These chemicals have documented insecticidal characteristics. To make acylsugars, the plants attach branched-chain and straight-chain fatty acyl groups to sugar backbones. While many steps of acylsugar synthesis pathways have been identified, several acylsugar metabolic genes remain unknown. In this study, we used comparative genomic approaches in two independent experiments: a differential gene expression analysis between high- and low-acylsugar-producing S. pennellii accessions, and another differential gene expression analysis between 10 high- and 10 low-acylsugar-producing F2 plants of S. pennellii LA 0716 and S. lycopersicum cv. VF36 cross, to further investigate the biosynthesis of acylsugar in S. pennellii. Differential gene expression analysis tools were used to identify known and novel candidate genes, including genes putatively encoding fatty acid synthases, acyl-activating enzymes, ATP binding cassette (ABC) transporters, and CO2 fixation proteins, that were positively correlated with acylsugar accumulation. When S. pennellii leaves were treated with an inhibitor of BCAA biosynthesis, expression of known and candidate genes was repressed in response to inhibitor in a concentration-dependent manner. We identified four genes, Sopen05g009610, Sopen07g006810, Sopen05g032580 and Sopen05g034770 that were common in two differentially expressed gene (DEG) sets collected from the two independent comparative transcriptomics experiments and were under positive selection. I confirmed two candidate genes, Sopen05g009610, encoding a component of a fatty acid synthase, and Sopen07g006810, encoding a small subunit of Rubisco, through virus-induced gene silencing (VIGS), to be involved in medium-chain fatty acids synthesis pathway and carbon fixation associated with acylsugar production, respectively. These results provide strong support for the involvement of novel candidate genes we identified in acylsugar biosynthesis, and validate our approach of combining differential gene expression and evolutionary analysis.
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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 | 0.000 | 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 | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".