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Diploidization and genome size change in allopolyploids is associated with differential dynamics of low‐ and high‐copy sequences
Author(s) -
RennyByfield Simon,
Kovarik Ales,
Kelly Laura J.,
Macas Jiri,
Novak Petr,
Chase Mark W.,
Nichols Richard A.,
Pancholi Mahesh R.,
Grandbastien MarieAngele,
Leitch Andrew R.
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12168
Subject(s) - biology , genome , polyploid , genome size , ploidy , genome evolution , genetics , gene duplication , plant evolution , evolutionary biology , nicotiana , concerted evolution , gene , solanaceae
Summary 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 N icotiana section R epandae , which arose via allopolyploidy (approximately 5 million years ago) involving relatives of N icotiana sylvestris and N icotiana obtusifolia . Subsequent speciation in Repandae has resulted in allotetraploids with divergent genome sizes, including N icotiana repanda and N icotiana 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 T y3/ G ypsy 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.