Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella
Bibliographic record
Abstract
BACKGROUND: The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development and sex determination have not been comprehensively studied and the lack of complete structure of mRNA transcripts limits further research. RESULTS: Here, we combined the methods of single-molecule long-read sequencing technology (IsoSeq) and RNA-seq to re-annotate the published DBM genome and present the genome-wide identification of alternative splicing (AS) associated with development and sex determination of DBM. In total, we identified ~ 13,900 genes (~ 77%) annotated in the DBM genome (version-2), resulting in the correction of 1586 wrongly annotated genes and identification of 78,000 previously unannotated transcripts. We also identified 1804 genes showing alternative splicing (AS) in each of the developmental stages and sexes, suggesting that AS events are ubiquitous in DBM. Comparative analyses showed that these AS events were rarely shared among developmental stages, indicating that they may play key specific roles in regulation of insect development. Further, we found 156 genes showing different AS events and expression patterns between males and females, linking them to potential functions in sex determination. CONCLUSION: Overall, the P. xylostella transcriptome provides the significant information about regulatory alternative splicing events, which are shown to be involved in development and sex determination. Our work presents a solid foundation to better understand the mechanism of post-transcriptional regulation, and offers wider insights into insect development and sex determination.
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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 | 0.000 | 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) | 0.001 | 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".