An intact, but dormant LTR retrotransposon defines a moderately-sized family in white spruce (Picea glauca)
Bibliographic record
Abstract
Within seed plants, the genomes of the conifer lineage are extraordinarily large and complex. While the evolutionary mechanisms driving this expansion are poorly understood, increasing evidence implicates retrotransposon activity as the driving force. We have isolated in targeted fashion and sequenced two independent white spruce genomic BAC clones for CYP701A24, involved in the biosynthesis of the phytohormone gibberellic acid. Sequence comparison showed little similarity between the two clones, one carrying the bona fide target CYP701A24 and the other an intronless fragment of a CYP701A24 pseudogene. In proximity of both CYP701A24 loci, we detected several signatures of the long terminal repeat (LTR) retrotransposon class. Sequence characterization identified one outstanding Ty3-gypsy class element, which was termed Picnicker1 for its size and degree of sequence conservation in the LTR. Representation of its homologous sequence in genomic amplicons and within the white spruce draft genome revealed that Picnicker1 is the founding member of a moderately sized family. Dating of the insertion event with the synonymous substitution rate applied to the nucleotide polymorphisms of the LTR suggested an age postdating major speciation in spruce. Independent support for an evolutionary recent incident was provided by an investigation of the genomic locus in a range of spruce species with increasing relatedness to white spruce, and in white spruce for a range of geographical origins. Transcript evidence revealed that related members of the family, but not Picnicker1 still flourish as part of the dynamic content in modern spruce genomes.
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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 | 0.000 | 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 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".