RNA-seq analysis of the mantle transcriptome from Mytilus edulis during a seasonal spawning event in deep and shallow water culture sites on the northeast coast of Newfoundland, Canada
Bibliographic record
Abstract
The blue mussel (Mytilus edulis) has global commercial and ecological importance both in wild and cultured conditions. However there is a qualitative and quantitative lack of knowledge of the molecular mechanisms associated with its reproductive physiology, especially with reference to environmental interactions. Here we initiated a transcriptomic analysis (RNA-sequencing (RNA-seq)) of the mantle from both sexes sampled during a seasonal spawning event and from two culture depths (shallow-5 m; deep- 15 m). Mantle libraries were produced from 3 males and 3 females sampled from each of two shallow sites and two deep sites for a total of 12 replicate male and 12 replicate female libraries (24 total libraries). Overall a total of 2.3 billion raw 100 base reads with an average of 96.5 million reads/library were obtained and assembled into 296,118 transcripts with an average length of 568 bp. Overall, 315 transcripts from male libraries and 25 from female libraries were found to be upregulated in deep water as compared to shallow (edgeR adjusted p value ≤ 0.05). Conversely, 126 transcripts from male libraries and 135 from female libraries were found to be significantly downregulated at the same depth. Thirteen transcripts were selected for qPCR validation based on importance in reproduction, antimicrobial defense and metabolism. Of these, 9 RNA-seq identified transcripts were shown by qPCR to be differentially expressed between groups: 2 were upregulated in deep compared with shallow water (dhx38, mt-co1), 2 were upregulated for female compared with male mantle (pias2, mapkap1) and 6 genes (fndc3a, acbd3, klhl10, ccnb3, armc4, mt-co1) showed to be upregulated in males compared to females. The majority of qPCR studied transcripts were identified as involved in gamete development based on the UniProt database. This study further characterizes the importance of the mantle transcriptome during reproductive activities of M. edulis.
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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 | 0.000 |
| Science and technology studies | 0.001 | 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".