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Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences.
Plant J 2013; 74(5):829-39PJ

Abstract

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.

Authors+Show Affiliations

Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23517128

Citation

Renny-Byfield, Simon, et al. "Diploidization and Genome Size Change in Allopolyploids Is Associated With Differential Dynamics of Low- and High-copy Sequences." The Plant Journal : for Cell and Molecular Biology, vol. 74, no. 5, 2013, pp. 829-39.
Renny-Byfield S, Kovarik A, Kelly LJ, et al. Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. Plant J. 2013;74(5):829-39.
Renny-Byfield, S., Kovarik, A., Kelly, L. J., Macas, J., Novak, P., Chase, M. W., ... Leitch, A. R. (2013). Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. The Plant Journal : for Cell and Molecular Biology, 74(5), pp. 829-39. doi:10.1111/tpj.12168.
Renny-Byfield S, et al. Diploidization and Genome Size Change in Allopolyploids Is Associated With Differential Dynamics of Low- and High-copy Sequences. Plant J. 2013;74(5):829-39. PubMed PMID: 23517128.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. AU - Renny-Byfield,Simon, AU - Kovarik,Ales, AU - Kelly,Laura J, AU - Macas,Jiri, AU - Novak,Petr, AU - Chase,Mark W, AU - Nichols,Richard A, AU - Pancholi,Mahesh R, AU - Grandbastien,Marie-Angele, AU - Leitch,Andrew R, Y1 - 2013/04/05/ PY - 2013/01/19/received PY - 2013/02/23/revised PY - 2013/03/01/accepted PY - 2013/3/23/entrez PY - 2013/3/23/pubmed PY - 2013/12/29/medline SP - 829 EP - 39 JF - The Plant journal : for cell and molecular biology JO - Plant J. VL - 74 IS - 5 N2 - 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. SN - 1365-313X UR - https://www.unboundmedicine.com/medline/citation/23517128/Diploidization_and_genome_size_change_in_allopolyploids_is_associated_with_differential_dynamics_of_low__and_high_copy_sequences_ L2 - https://doi.org/10.1111/tpj.12168 DB - PRIME DP - Unbound Medicine ER -