Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

Abstract

Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome sequence remains incompletely assembled. We report a 4.2Gb telomere-to-telomere gap-free N. tabacum reference genome phased into two subgenomes (subS/subT) , revealing differential evolutionary trajectories between two subgenomes marked by a rapid divergence in paternal T-genome, especially for heterochromatic centromeric regions. To understand the evolutionary dynamics of tobacco centromeres following polyploidization, we characterize the centromere architecture in tetraploid N. tabacum and its diploid progenitors, demonstrating clear subgenomic diversification and repositioning of centromeres during speciation and allopolyploidization. These findings enrich our knowledge on centromere paradox in polyploid genomes.