Plastid Genome Evolution in the Parasitic Genera Cuscuta (Convolvulaceae) and Krameria (Krameriaceae)
Bibliographic record
Abstract
Almost all plants are primary producers and many of their phenotypic and genotypic features are centered on the ability to conduct photosynthesis. Variation in these features is rare across green plants due to the degree of selective pressure imposed by primary production. This is particularly true for plastid genomes (plastomes) given that chloroplasts are the primary site of photosynthesis in the cell and that plastomes encode key portions of the photosynthetic apparatus.In only a handful of embryophyte lineages, however, a heterotrophic lifestyle has evolved and reliance on photosynthesis for resource acquisition is reduced or completely absent. In these plants, the selective pressure imposed by primary production is lifted and previously conserved features are able to evolve more freely, including the plastid genome. The genus Cuscuta is one such lineage. It contains c. 200 obligate branch parasite species, diverse in terms of the degree of their heterotrophy: some can conduct limited photosynthesis whilst others are entirely nonphotosynthetic. In chapters 2-4, I assembled and analyzed plastomes from each section of Cuscuta in order to comprehensively characterize the patterns in their evolution across the genus. I found that most species retain the bulk of their photosynthesis genes and, therefore, at least some aspect of the bioenergetic pathway remains available for them to use. In plants forming two clades within Cuscuta, however, there was a wholesale loss of plastid genes encoding the photosynthetic machinery. The genus Krameria contains 18 species of root hemiparasites and they, like Cuscuta, represent an additional independent transition from autotrophy to heterotrophy. In chapter 5, I assembled the plastid genome of one Krameria species and analyzed it along with two previously reported plastid genomes from the group. I found that these species exhibit sweeping retention of plastid genes, unprecedented amongst parasitic angiosperms, and do not appear to have been impacted by the transition to heterotrophy the same way that other parasitic lineages have been. By characterizing plastomes in these two genera, my thesis contributes to our growing understanding of how heterotrophic plants, and genomes, change due to a reduction (or complete loss) of the selective pressure imposed by photosynthesis.
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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 | 0.000 |
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".