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Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations. We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural  Nicotiana tabacum  with diploid progenitors  N. tomentosiformis  (paternal progenitor) and  N. sylvestris  (maternal progenitor). Using next generation sequencing, a recently developed graph-based repeat identification pipeline, Southern blot and fluorescence  in situ  hybridisation (FISH) we characterise two highly repetitive DNA sequences ( Nic CL3 and  Nic CL7/30). Analysis of two independent high-throughput DNA sequencing datasets indicates  Nic CL3 forms 1.6–1.9% of the genome in  N. tomentosiformis , sequences that occur in multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based on sequencing depth, indicate  Nic CL3 is almost absent in  N. sylvestris  and has been dramatically reduced in copy number in the allopolyploid  N. tabacum . Surprisingly elimination of  Nic CL3 is repeated in some synthetic lines of  N. tabacum  in their forth generation. The retroelement  Nic CL7/30, which occurs interspersed with  Nic CL3, is also under-represented but to a much lesser degree, revealing targeted elimination of the latter. Analysis of paired-end sequencing data indicates the tandem component of  Nic CL3 has been preferentially removed in natural  N. tabacum , increasing the proportion of the dispersed component. This occurs across multiple blocks of discontinuous repeats and based on the distribution of nucleotide similarity among  Nic CL3 units, was concurrent with rounds of sequence homogenisation.

Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum