Differential Gene Expression and Unbalanced Homeolog Expression Bias in 4 Million-Year-Old Allopolyploids of <i>Nicotiana</i> Section <i>Repandae</i>

Allopolyploidy, a phenomenon prevalent in angiosperms involving hybridization and whole-genome duplication, results in species with multiple subgenomes, altering genome structure and gene expression, leading to novel phenotypes. Allopolyploids often experience unbalanced homeolog expression bias, the preferential expression of homeologs from one of the two progenitor genomes. To explore the consequences of allopolyploidy and unbalanced homeolog expression bias, we investigate global gene expression and the fate of homeologs in Nicotiana (Solanaceae). We focus on Nicotiana section Repandae, including three allotetraploid species, Nicotiana nudicaulis, N. repanda, and N. stocktonii, derived from diploid progenitors N. sylvestris and N. obtusifolia ∼4.3 Ma. We identify genes with differential expression and investigate expression of candidate genes for flower size variation. Our results show expression differences with the allopolyploids intermediate between the two progenitor species, with a slight bias toward N. obtusifolia. Moreover, we demonstrate unbalanced homeolog expression bias toward the N. obtusifolia subgenome across developmental stages in the allopolyploids, with a stronger bias in N. nudicaulis. In contrast, unbalanced homeolog expression bias shifts toward N. sylvestris for flower size genes in N. nudicaulis, showing that genes involved in particular phenotypes can display different patterns of unbalanced homeolog expression than the overall transcriptome. We also see differential expression of several known flower size genes across corolla developmental stages. Our results highlight the role of unbalanced homeolog expression bias in shaping the evolutionary trajectory of Nicotiana species and provide a foundation for future research into the ecological and evolutionary implications of allopolyploidy in flowering plants.