Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes
Bibliographic record
Abstract
The legume family originated ca. 60-65 million years ago and soon diversified into at least six lineages (now extant subfamilies). The signal of whole genome duplications (WGD) is apparent in species sampled from all six subfamilies. The early diversification has posed difficulties for resolving the legume backbone structure and the timing of WGDs, especially in Caesalpinioideae where the diversification and WGD signals coincide. In this study, we report the genome sequences and annotations for Cercis canadensis (Cercidoideae) and Chamaecrista fasciculata (Caesalpinioideae) to help resolve the timings of WGDs relative to subfamily origins and the ancestral legume karyotype. Analyses of genome assemblies from four subfamilies within Fabaceae show that the last common ancestor of all legumes likely had seven chromosomes, with a genome structure similar to the extant Cercis genome. The retained karyotype structure, the lack of a WGD in the last 100+ Mya (Cercis and the lineage leading to it following the eudicot γ whole-genome triplication), and the unusually slow rates of nucleotide substitution and structural evolution in the Cercis genome underscore its utility as a genomic proxy for the last common ancestor of all legume species. Our analysis supports an allopolyploid origin of Caesalpinioideae, with progenitors from lineages along the backbone of the legume phylogeny. Rapid diversification and the inferred allopolyploid origin of Caesalpinioideae provide a partial explanation for the difficulty in resolving the backbone of the legume phylogeny and early Caesalpinioideae diversification.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 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 teacher head, 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".