Dramatic Change in Function and Expression Pattern of a Gene Duplicated by Polyploidy Created a Paternal Effect Gene in the Brassicaceae
Bibliographic record
Abstract
New gene formation by polyploidy has been an ongoing process during the evolution of various eukaryotes that has contributed greatly to the large number of genes in their genomes. After duplication, some genes that are retained can acquire new functions or expression patterns, or subdivide their functions or expression patterns between duplicates. Here, we show that SHORT SUSPENSOR (SSP) and Brassinosteroid Kinase 1 (BSK1) are paralogs duplicated by a polyploidy event that occurred in the Brassicaceae family about 23 Ma. SSP is involved in paternal control of zygote elongation in Arabidopsis thaliana by transcription in the sperm cells of pollen and then translation in the zygote, whereas BSK1 is involved in brassinosteroid signal transduction. Comparative analysis of expression in 63 different organs and developmental stages revealed that BSK1 and SSP have opposite expression patterns in pollen compared with all other parts of the plant. We determined that BSK1 retains the ancestral expression pattern and function. Thus, SSP has diverged in function after duplication from a component of the brassinosteroid signaling pathway to a paternal regulator of the timing of zygote elongation. The ancestral function of SSP was lost by deletions in the kinase domain. Our sequence rate analysis revealed that SSP but not BSK1 has experienced a greatly accelerated rate of amino acid sequence changes and relaxation of purifying selection. In addition, SSP has been duplicated to create a new gene (SSP-like1) with a completely different expression pattern, a shorter coding sequence that has lost a critical functional domain, and a greatly accelerated rate of amino acid sequence evolution along with evidence for positive selection, together indicative of neofunctionalization. This study illustrates two dramatic examples of neofunctionalization following gene duplication by complete changes in expression pattern and function. In addition, our findings indicate that paternal control of zygote elongation by SSP is an evolutionarily recent innovation in the Brassicaceae family.
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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 | 0.000 | 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) | 0.001 | 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".