Evolutionary dynamics and functional characterization of Jasmonate ZIM-domain (<i>JAZ</i>) genes across <i>Camellia sinensis</i> pan-genome
Bibliographic record
Abstract
Jasmonate ZIM-domain (JAZ) proteins regulate critical processes in plants, including growth, development, secondary metabolism, and responses to biotic and abiotic stresses. Previous studies primarily focused on single reference genomes, neglecting gene presence-absence variations (PAV) across populations. Investigating the <italic>JAZ</italic> gene family at the pan-genomic scale is thus essential to fully understand its evolutionary and functional dynamics in tea plants. Here, 22 high-quality <italic>Camellia sinensis</italic> genomes were analyzed, and 21 <italic>JAZs</italic> exhibiting substantial presence-absence variability were identified. These included two core genes (present in all 22 genomes), three near-core genes (present in 20–21 genomes), ten dispensable genes (present in 2–19 genomes), and six private genes (unique to single genomes). Phylogenetic analysis categorized these <italic>JAZs</italic> into five distinct groups, aligning with the <italic>AtJAZ</italic> family. Selection pressure analysis revealed positive selection (<italic>K</italic>a/<italic>K</italic>s > 1) acting on <italic>CsJAZ1</italic>, <italic>CsJAZ8</italic>, and <italic>CsJAZ9</italic>, suggesting adaptive roles during tea domestication. Structural variants (SVs) significantly impacted gene expression and structural integrity; notably, <italic>CsJAZ4</italic>, <italic>CsJAZ9</italic>, and <italic>CsJAZ12</italic> exhibited differential expression when affected by SVs. RNA-seq analysis across four tissues from the 22 tea plant cultivars showed consistently high expression of <italic>CsJAZ1</italic>, <italic>CsJAZ2</italic>, <italic>CsJAZ6</italic>, <italic>CsJAZ9</italic>, <italic>CsJAZ13</italic>, and <italic>CsJAZ14</italic>, highlighting their potential fundamental roles. This study elucidates the <italic>JAZ</italic> gene family's evolutionary complexity and functional versatility within the tea plant pan-genome. These findings provide valuable insights for future research into <italic>CsJAZ</italic> functions and serve as a model for pan-genomic analyses of gene families in other plant species.
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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 | 0.000 |
| 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) | 0.001 | 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".