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dc.contributor.authorRenny-Byfield, Sen_US
dc.contributor.authorKovarik, Aen_US
dc.contributor.authorKelly, LJen_US
dc.contributor.authorMacAs, Jen_US
dc.contributor.authorNovak, Pen_US
dc.contributor.authorChase, MWen_US
dc.contributor.authorNichols, RAen_US
dc.contributor.authorPancholi, MRen_US
dc.contributor.authorGrandbastien, MAen_US
dc.contributor.authorLeitch, ARen_US
dc.description.abstractSummary Recent advances have highlighted the ubiquity of whole-genome duplication (polyploidy) in angiosperms, although subsequent genome size change and diploidization (returning to a diploid-like condition) are poorly understood. An excellent system to assess these processes is provided by Nicotiana section Repandae, which arose via allopolyploidy (approximately 5 million years ago) involving relatives of Nicotiana sylvestris and Nicotiana obtusifolia. Subsequent speciation in Repandae has resulted in allotetraploids with divergent genome sizes, including Nicotiana repanda and Nicotiana nudicaulis studied here, which have an estimated 23.6% genome expansion and 19.2% genome contraction from the early polyploid, respectively. Graph-based clustering of next-generation sequence data enabled assessment of the global genome composition of these allotetraploids and their diploid progenitors. Unexpectedly, in both allotetraploids, over 85% of sequence clusters (repetitive DNA families) had a lower abundance than predicted from their diploid relatives; a trend seen particularly in low-copy repeats. The loss of high-copy sequences predominantly accounts for the genome downsizing in N. nudicaulis. In contrast, N. repanda shows expansion of clusters already inherited in high copy number (mostly chromovirus-like Ty3/Gypsy retroelements and some low-complexity sequences), leading to much of the genome upsizing predicted. We suggest that the differential dynamics of low- and high-copy sequences reveal two genomic processes that occur subsequent to allopolyploidy. The loss of low-copy sequences, common to both allopolyploids, may reflect genome diploidization, a process that also involves loss of duplicate copies of genes and upstream regulators. In contrast, genome size divergence between allopolyploids is manifested through differential accumulation and/or deletion of high-copy-number sequences. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.en_US
dc.description.sponsorshipThe work was partially supported by the Czech Science Foundation (P501/13/10057S and P501/12/G090).en_US
dc.format.extent829 - 839en_US
dc.relation.ispartofPlant Journalen_US
dc.titleDiploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequencesen_US
pubs.notesNo embargoen_US

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