The Complete Plastid Genome of Neottia bifolia (Raf.) Baumbach (Orchidaceae): Insights Into Chlorophyllous and Achlorophyllous Plastid Genomes
Bibliographic record
Abstract
Neottia bifolia is a small, terrestrial orchid distributed across the southeastern United States and northward up the Atlantic coast into Canada. The genus is well-studied as a model for the evolution of mycoheterotrophy, having both chlorophyllous and putatively achlorophyllous taxa. Despite this, the photosynthetic species, N. bifolia is relatively understudied. We provide results from the sequencing, assembly, and annotation of the complete plastid genome of N. bifolia and examine some evolutionary trends in the genus, using the 10 additional complete Neottia plastid genomes available on GenBank. We find that the plastid genome of N. bifolia is 156,533 base pairs in length with 130 protein-coding genes, including 38 tRNA genes and eight rRNA genes. We find a similar number of rRNAs and tRNAs across the genus, but significantly fewer protein coding genes and an overall smaller plastid genome size in the mycoheterotrophic species. We find support for the monophyly of the mycoheterotrophic species. The placement of N. bifolia varies slightly between inferences, but the species is most frequently placed in a clade with Neottia cordata, Neottia japonica, and Neottia suzuki.
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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 | 0.001 | 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 | 0.001 |
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".