A comparative survey, by expressed sequence tag analysis, of genes expressed in peach leaves infected with<i>Plum pox virus</i>(PPV) and free from PPV
Bibliographic record
Abstract
Plum pox virus (PPV), genus Potyvirus, is a serious threat to the fruit and ornamental horticulture industry in Canada. Genomic resources of its natural hosts, Prunus spp., currently available to researchers studying PPV are very poor. Systematic sequencing of expressed sequence tags (ESTs) can be used as a discovery base for genes associated with PPV infection, replication, and symptom development. Here we describe the construction of two directional, size-selected cDNA libraries derived from PPV-infected and PPV-free peach leaves, and the generation of 3839 ESTs. Based on their partial sequences and putative functions, the ESTs are classified into 611 clusters and 1153 singletons. About 65.36% of the genes (2509 ESTs) show homology to genes from other organisms, and 34.64% of cDNAs (1330 ESTs) have no matches in the GenBank database. Comparison analyses suggest that genes involved in defence, cellular transport, development, protein synthesis, proteins with binding function in the PPV-infected peach leaf tissue are more active than those in PPV-free leaves. Moreover, a number of gene transcripts, including β-1,3- glucanase, cytochrome-P450-like protein, cytochrome P450 monooxygenase, heat-shock protein 70, thioredoxin, alcohol dehydrogenase, catalase, cysteine protease inhibitor, translation factor EF-1α, and pathogenesis-related protein (PR1) are highly prevalent only in the PPV-infected peach leaf. Consistent with results in several recent publications from other laboratories, our finding supports the view that positive-stranded viruses may elicit common responses in susceptible plants. The results of this study help better understand the molecular mechanisms associated with susceptibility to PPV disease in Prunus persica. and provide a studying point for the development of novel strategies to control the virus.
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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) | 0.000 | 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 | 0.000 |
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 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".