Amplifying long transcripts of ryanodine receptors of five agricultural pests by transcriptome analysis and gap filling
Bibliographic record
Abstract
Ryanodine receptor (RyR) is an intracellular calcium release channel that plays a key role in excitation contraction coupling. Insect RyR is the target of diamide insecticides. Better understanding of insect RyR is necessary for studying the molecular mode of action and potential resistance mechanism of diamide insecticides. However, molecular manipulation of the full RyR gene is difficult because of its length (approximately 15 kb). At present, RyR genes have been reported only in a limited number of insects. Here, we developed an efficient strategy to amplify full-length transcripts of insect RyR genes. First, we searched the transcriptomes of five insects, Bemisia tabaci, Cnaphalocrocis medinalis, Chilo suppressalis, Laodelphgax striatellus, and Plutella xylostella, yielding 85 RyR contigs in total. Second, the relative positions of these contigs in RyR transcripts were determined by aligning them with 12 well-annotated RyRs. Third, we designed primers to fill gaps between contigs and used rapid amplification of cDNA ends (RACE) to amplify both 5'- and 3'-ends. Last, we assembled all fragments into long transcripts. As a result, full-length transcripts of three insects, C. suppressalis, L. striatellus, and P. xylostella, were obtained. The RyR transcript of B. tabaci was near full length, containing an intact ORF. Northern blot analysis indicated that RyR genes were expressed in all five insects. Sequence analyses showed that the amplified insect segments contained typical RyRs characteristics, such as EF-hand, motif GVRAGGGIGD, and six transmembrane domains. Seven lepidopteran-specific amino acid residues were found to be located in the C-terminal region of RyR proteins, which might be associated with the specificity of RyRs to diamide insecticides.
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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 | 0.000 |
| 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 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".