Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids
Bibliographic record
Abstract
Abstract Understanding the molecular evolution of genes involved in parasite adaptation and the role of transposable elements (TEs) in driving their diversification is key to unraveling how populations adapt to their environments. In phytophagous insects like aphids, olfactory (OR) and gustatory receptor (GR) genes are crucial for host recognition, yet their post-duplication evolution remains insufficiently explored. Here, we analyzed 521 OR and 399 GR genes, alongside TEs, across 12 aphid genomes with varying host ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates, driven by gene family expansions linked to host interaction, including lipid metabolism, immune function, and transposase activity. The evolution of OR and GR genes post-duplication was shaped by diversifying selection, with bursts of positive selection followed by long periods of purifying selection, consistent with adaptation to new hosts. OR and GR genes originated from proximal and tandem duplications, with younger TE activity enriched near these genes compared to other genomic regions, suggesting a role for TEs in catalyzing tandem duplications and fueling diversification. The star-like topology of the OR phylogenetic tree, low synteny, and recent TE activity around OR genes support a faster evolutionary rate for ORs than GRs - a trend observed in other insect taxa. This study provides insights into molecular mechanisms underlying host adaptation in aphids and presents the first high-quality genome assembly of Dysaphis plantaginea , a major apple pest, with a comprehensive annotation of chemosensory genes and TEs. These resources offer a foundation for research on aphid genome evolution, insect–plant interactions.
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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 | 0.001 |
| 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) | 0.002 | 0.001 |
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".