The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured
Bibliographic record
Abstract
BACKGROUND: Loss of photosynthesis has occurred independently in several plant and algal lineages, and represents a major metabolic shift with potential consequences for the content and structure of plastid genomes. To investigate such changes, we sequenced the complete plastid genome of the parasitic, non-photosynthetic green alga, Helicosporidium. RESULTS: The Helicosporidium plastid genome is among the smallest known (37.5 kb), and like other plastids from non-photosynthetic organisms it lacks all genes for proteins that function in photosynthesis. Its reduced size results from more than just loss of genes, however; it has little non-coding DNA, with only one intron and tiny intergenic spaces, and no inverted repeat (no duplicated genes at all). It encodes precisely the minimal complement of tRNAs needed to translate the universal genetic code, and has eliminated all redundant isoacceptors. The Helicosporidium plastid genome is also highly structured, with each half of the circular genome containing nearly all genes on one strand. Helicosporidium is known to be related to trebouxiophyte green algae, but the genome is structured and compacted in a manner more reminiscent of the non-photosynthetic plastids of apicomplexan parasites. CONCLUSION: Helicosporidium contributes significantly to our understanding of the evolution of plastid DNA because it illustrates the highly ordered reduction that occurred following the loss of a major metabolic function. The convergence of plastid genome structure in Helicosporidium and the Apicomplexa raises the interesting possibility that there are common forces that shape plastid genomes, subsequent to the loss of photosynthesis in an organism.
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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) | 0.002 | 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".