Polyploidy and Genome Size Evolution in Nicotiana

Evolution and change in copy-number of repetitive DNA associated with polyploidy can be analysed using next generation sequencing data and  genome-skimming approaches. In allopolyploid Nicotiana species we compare genomic compositions with diploids that most closely resemble the actual progenitors. In Nicotiana tabacum (formed <0.2 mya), we identified a bias towards removal of paternally derived repeats in conjunction with an overall reduction in the repetitive fraction of the genome. Surprisingly, similar sequence loss are observed in synthetic lines after only four generations. Older polyploids are represented by four species in Nicotiana section Repandae, which arose via a single allopolyploid event c. 5 mya. We analysed two in detail, N. repanda and N. nudicaulis, the later showing genome upsizing and the former genome downsizing. Unexpectedly, in both allotetraploids, over 85% of repetitive DNA families (clusters) were at lower abundance than predicted based on their abundance in the diploids; a trend seen predominantly in low-copy repeats. Sequence specific amplification polymorphism analysis revealed a loss of paternally inherited bands, echoing patterns observed in N. tabacum. In N. nudicaulis it is the loss of high-copy sequences, which accounts for most of the 14.7% reduction in the genome size from expectation. In contrast, N. repanda shows expansion of clusters already inherited in high copy-number (mostly chromovirus-like LTR retroelements), leading to a 26.0% increase in genome size. Thus genome diploidisation following polyploidy appears to involve processes that erode low copy-number nuclear DNA, whereas genome size divergence is dominated by differential removal and/or accumulation of high copy-number sequences.