Characterizing chloroplast genomes and inferring maternal divergence of the Triticum–Aegilops complex
Bibliographic record
Abstract
The Triticum (wheat)-Aegilops (goatgrass) complex has been extensively studied, but the evolutionary history of polyploid wheats has not been fully elucidated. The chloroplast (cp) with maternal inheritance and homoplasy can simplify the sequence-based evolutionary inferences, but informative inferences would require a complete and accurate cp genome sequence. In this study, 16 cp genomes representing five Aegilops and 11 Triticum species and subspecies were sequenced, assembled and annotated, yielding five novel circular cp genome sequences. Analyzing the assembled cp genomes revealed no marked differences in genome structure and gene arrangement across the assayed species. A polymorphism analysis of 72 published cp genome sequences representing 10 Aegilops and 15 Triticum species and subspecies detected 1183 SNPs and 1881 SSRs. More than 80% SNPs detected resided on the downstream and upstream gene regions and only 2.78% or less SNPs were predicted to be deleterious. The largest nucleotide diversity was observed in the short single-copy genomic region. Relatively weak selection pressure on cp coding genes was detected. Different phylogenetic analyses confirmed that the maternal divergence of the Triticum-Aegilops complex had three deep lineages each representing a diploid species with nuclear A, B, or D genome. Dating the maternal divergence yielded age estimates of divergence that matched well with those reported previously. The divergence between emmer and bread wheats occurred at 8200-11,200 years ago. These findings are useful for further genomic studies, provide insight into cp genome evolvability and allow for better understanding of the maternal divergence of the Triticum-Aegilops complex.
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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 | 0.001 |
| 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) | 0.000 | 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".