Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences

Simon Renny-Byfield, Ales Kovarik, Laura J Kelly, Jiri Macas, Petr Novak, Mark W Chase, Richard A Nichols, Mahesh R Pancholi, Marie-Angele Grandbastien, Andrew R Leitch

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)829-39
Number of pages11
JournalThe Plant Journal
Issue number5
Publication statusPublished - Jun 2013


  • Cluster Analysis
  • Diploidy
  • Evolution, Molecular
  • Genetic Speciation
  • Genetic Variation
  • Genome Size
  • Genome, Plant
  • In Situ Hybridization
  • Polyploidy
  • Segmental Duplications, Genomic
  • Species Specificity
  • Time Factors
  • Tobacco


Dive into the research topics of 'Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences'. Together they form a unique fingerprint.

Cite this