Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome remains incompletely assembled. We present a 4.2-Gb telomere-to-telomere, gap-free, and phased genome assembly. This assembly reveals distinct evolutionary trajectories between the two subgenomes, particularly within heterochromatic centromeric regions. Consistent with the rapid sequence divergence of the T subgenome, we observe pronounced differences in DNA methylation landscapes between subgenomes. To understand centromere evolution following polyploidization, we characterize centromere architecture in tetraploid Nicotiana tabacum and its diploid progenitors, uncovering asymmetric subgenomic diversification and frequent centromere repositioning. These findings provide new insights into dynamic evolution of centromeres in polyploid genomes.