Endosymbiotic Gene Transfer in the Nucleomorph containing organisms Bigelowiella natans and Guillardia theta
Bibliographic record
Abstract
Mitochondria and chloroplasts are eukaryotic organelles that were acquired through endosymbiosis. In the case of the mitochondrion, a heterotrophic cell engulfed and retained an alpha-proteobacterium. The engulfed bacterium, or endosymbiont, underwent extensive cellular and genetic integration with its host, thereby becoming an organelle. Chloroplasts are derived from the engulfment and retention of a photosynthetic cyanobacterium that also experienced loss of cellular functions and genetic material. Although mitochondria and chloroplasts retain their own genomes, most of the proteins that function in these organelles are encoded by genes that were transferred to the nucleus in a process known as Endosymbiotic Gene Transfer (EGT).\n\nChloroplasts in plants, green algae and red algae are known as primary plastids. Other photosynthetic organisms have secondary plastids that were acquired by engulfing and retaining a primary plastid-bearing alga. In the process, the nucleus of the engulfed alga underwent EGT (and presumably gene loss) to such an extent that it disappeared completely except in two lineages, cryptophytes and chlorarachniophytes, which retain a highly reduced and miniaturized form known as a nucleomorph. \n\nTo understand the process of EGT and endosymbiosis in general, the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans were sequenced. In the case of G. theta its nucleomorph is of red algal origin while the nucleomorph of B. natans is derived from a green algal endosymbiont. \n\nPrior to the nuclear genome projects the genomes of the three organelles – plastid, mitochondrion, nucleomorph – had already been sequenced. This allowed investigation of recent transfers of organellar DNA to the nucleus. Mitochondrial transfers to the nucleus are still occurring in both organisms but transfers of plastid and nucleomorph DNA are not. The nucleomorph genomes of B. natans and G. theta appear ‘frozen’, unable to undergo EGT and thus unable to disappear as they have in all other lineages with secondary plastids. The creation of a spliceosomal intron from transferred organellar DNA was investigated.\n\nI also investigated nuclear genes whose encoded proteins appear to function in the mitochondrion. 833 putatively mitochondrial targeted proteins were identified in G. theta and 720 in B. natans.
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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 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| 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".