Genome-Wide Analyses of Copy Number Variants in 751 <i>Populus trichocarpa</i> Individuals From Natural Populations
Bibliographic record
Abstract
Copy number variations (CNVs), including duplications and deletions of the genome ranging up to 1 Mb, are an important contributor to genomic variation, and may influence phenotypic variation. They are relatively understudied compared with single nucleotide polymorphisms despite affecting a higher proportion of the genome. Using whole genome sequencing data and RNA-sequencing data, we identified and characterized the natural diversity of CNVs across the native range of Populus trichocarpa and the effects of CNVs on gene expression. We analyzed whole genome sequencing data of 751 P. trichocarpa individuals to identify CNVs, analyzed their size, distribution and population structure. We also examined gene expression with RNA-sequencing data of leaf and xylem tissues for 390 individuals. We found 11,501 duplications and 22,839 deletions covering a major percentage of the genome. Genes overlapping with CNVs were enriched in important biological processes such as reproduction, cellulose production, and defense. Analysis of CNV genotypes with expression data showed that a minority of genes overlapping CNVs have a strong correlation of expression level with copy number. Those genes were significantly enriched in stress-related responses. Our identified CNVs provide insights into the extent, characteristics, and diversity of CNVs in wild populations of P. trichocarpa and the effects of CNVs on gene expression.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 |
| 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 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".