Structured, inbred, and plastic: the genome and population genetics of the weed false cleavers (<i>Galium spurium</i>)
Bibliographic record
Abstract
Abstract False cleavers ( Galium spurium L.) is an aggressive weed from the Rubiaceae. Here we assemble a chromosome-scale draft of its genome, laying the foundations for determining the genetic basis of auxinic herbicide resistance and for systematic research into its polyphyletic genus. We use the genome to examine the population genetics of material from the Canadian Prairies and, in concert with a common greenhouse experiment, to examine whether the phenotypic variation observed in the field results primarily from genetic or environmental factors. The genome assembly covers approximately 85% of G. spurium ’s expected 360-Mbp genome size, with 94% of BUSCO (Benchmarking Universal Single-Copy Orthologs) genes complete and most single copy (89%). Approximately 37% of the genome is repetitive elements and 35,540 genes were annotated using RNA-seq data, including 100 homologues for genes involved in, or potentially involved in, herbicide resistance. The genome shows strong synteny with other members of the Rubiaceae, including smooth bedstraw ( Cruciata laevipes Opiz) and robusta coffee [ Coffea canephora (Pierre ex Froehner]. Double-digested RAD-seq data for the 19 populations from the Canadian Prairies indicated that G. spurium has high levels of population structure (F ST = 0.54) and inbreeding (F IS = 0.86) with low levels of hetrozygosity (H O = 0.02) and nucleotide diversity (π = 0.0003). Variation in flowering time and seed weight largely overlapped among populations grown in the greenhouse. A redundancy analysis investigating genotype–phenotype associations showed few associations between single-nucleotide polymorphism (SNP) variation and these characteristics. In contrast, the majority of SNPs under selection were associated with mericarp hook density. This suggests that for most traits, environmental variation rather than genetic variation likely underlies phenotypic differences observed in the field. Several genes of interest, including several homologues involved in the assembly of the Skp1-Cullin-F-Box IR1/AFB E3 ubiquitin ligase complex (e.g., CAND1 , ECR1 ), are located in areas of the genome with evidence of selection and are targets for further investigation.
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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) | 0.000 | 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 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".