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

摘要: Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms can result genomic, epigenetic transcriptomic perturbations. We examine immediate effects allopolyploidy on repetitive DNA by comparing genomes synthetic natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) sylvestris (maternal progenitor). Using next generation sequencing, recently developed graph-based repeat identification pipeline, Southern blot fluorescence situ (FISH) we characterise two highly sequences (NicCL3 NicCL7/30). Analysis independent high-throughput sequencing datasets indicates NicCL3 forms 1.6-1.9% genome tomentosiformis, that occur multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based depth, indicate is almost absent been dramatically reduced copy number allopolyploid tabacum. Surprisingly elimination repeated some lines their forth generation. The retroelement NicCL7/30, which occurs interspersed NicCL3, also under-represented but to much lesser degree, revealing targeted latter. paired-end data component preferentially removed tabacum, increasing proportion dispersed component. This across multiple blocks repeats distribution nucleotide similarity among units, was concurrent rounds sequence homogenisation.