<scp>V9</scp> Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada
Bibliographic record
Abstract
ABSTRACT Short amplicon sequencing is a commonly used method to study the diversity of organisms in various habitats. The hypervariable regions of the small subunit rRNA gene (18S rDNA) are the most general barcodes for eukaryotes, which can provide detailed taxonomic information across a wide range of eukaryotic diversity. However, some organisms are often missed by universal primers, which have difficulty amplifying their barcodes. In this study, specific primers were designed for the amplification of the highly diverse 18S‐V9 region of the Euglenozoa and Metamonada groups. The performance of the newly designed primers—V9Eug and V9Meta—was compared with the universal V9 primer on cultured communities derived from a range of freshwater environments of the Soos Natural Reserve and the Slavkov Forest in the Czech Republic. The V9Eug primer was more specific with Euglenozoa representing 91.8% of reads and 57.0% of OTUs, while the V9Meta primer showed lower specificity with only 48.4% of reads and 19.7% of OTUs assigned to Metamonada. Both the Euglenozoa and Metamonada primer pairs significantly improved recovery of their target groups compared to the universal V9 primer pair, detecting 2.7 and 1.8 times more OTUs, respectively. These results provide a more sensitive protocol for studying the diversity of these eukaryotic taxa.
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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".