Selaginella Genome Analysis – Entering the “Homoplasy Heaven” of the MADS World
Bibliographic record
Abstract
In flowering plants, arguably the most significant transcription factors regulating development are MADS-domain proteins, encoded by Type I and Type II MADS-box genes. Type II genes are divided into the MIKC(C) and MIKC* groups. In angiosperms, these types and groups play distinct roles in the development of female gametophytes, embryos, and seeds (Type I); vegetative and floral tissues in sporophytes (MIKC(C)); and male gametophytes (MIKC*), but their functions in other plants are largely unknown. The complete set of MADS-box genes has been described for several angiosperms and a moss, Physcomitrella patens. Our examination of the complete genome sequence of a lycophyte, Selaginella moellendorffii, revealed 19 putative MADS-box genes (13 Type I, 3 MIKC(C), and 3 MIKC*). Our results suggest that the most recent common ancestor of vascular plants possessed at least two Type I and two Type II genes. None of the S. moellendorffii MIKC(C) genes were identified as orthologs of any floral organ identity genes. This strongly corroborates the view that the clades of floral organ identity genes originated in a common ancestor of seed plants after the lineage that led to lycophytes had branched off, and that expansion of MIKC(C) genes in the lineage leading to seed plants facilitated the evolution of their unique reproductive organs. The number of MIKC* genes and the ratio of MIKC* to MIKC(C) genes is lower in S. moellendorffii and angiosperms than in P. patens, correlated with reduction of the gametophyte in vascular plants. Our data indicate that Type I genes duplicated and diversified independently within lycophytes and seed plants. Our observations on MADS-box gene evolution echo morphological evolution since the two lineages of vascular plants appear to have arrived independently at similar body plans. Our annotation of MADS-box genes in S. moellendorffii provides the basis for functional studies to reveal the roles of this crucial gene family in basal vascular plants.
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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".