Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

Abstract

Each mode of gene duplication (tandem, tetraploid, segmental, transpositional) retains genes in a biased manner. A reciprocal relationship exists between plant genes retained postpaleotetraploidy versus genes retained after an ancient tandem duplication. Among the models (subfunctionalization, neofunctionalization, balanced gene drive) and ideas that might explain this relationship, only balanced gene drive predicts reciprocity. The gene balance hypothesis explains that more “connected” genes—by protein-protein interactions in a heteromer, for example—are less likely to be retained as a tandem or transposed duplicate and are more likely to be retained postpaleotetraploidy; otherwise, selectively negative dosage effects are created. Biased duplicate retention is an instant and neutral by-product, a spandrel, of purifying selection. Balanced gene drive expanded plant gene families, including those encoding proteasomal proteins, protein kinases, motors, and transcription factors, with each paleotetraploidy, which could explain trends involving complexity. Balanced gene drive is a saltation mechanism in the mutationist tradition.