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Impact of transposable elements on genome structure and evolution in bread wheat.
Genome Biol. 2018 08 17; 19(1):103.GB

Abstract

BACKGROUND

Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.

RESULTS

The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.

CONCLUSIONS

Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.

Authors+Show Affiliations

Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.No affiliation info availablePGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany. School of Life Sciences, Technical University Munich, Munich, Germany.GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France. frederic.choulet@inra.fr.

Pub Type(s)

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

Language

eng

PubMed ID

30115100

Citation

Wicker, Thomas, et al. "Impact of Transposable Elements On Genome Structure and Evolution in Bread Wheat." Genome Biology, vol. 19, no. 1, 2018, p. 103.
Wicker T, Gundlach H, Spannagl M, et al. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol. 2018;19(1):103.
Wicker, T., Gundlach, H., Spannagl, M., Uauy, C., Borrill, P., Ramírez-González, R. H., De Oliveira, R., Mayer, K. F. X., Paux, E., & Choulet, F. (2018). Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biology, 19(1), 103. https://doi.org/10.1186/s13059-018-1479-0
Wicker T, et al. Impact of Transposable Elements On Genome Structure and Evolution in Bread Wheat. Genome Biol. 2018 08 17;19(1):103. PubMed PMID: 30115100.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Impact of transposable elements on genome structure and evolution in bread wheat. AU - Wicker,Thomas, AU - Gundlach,Heidrun, AU - Spannagl,Manuel, AU - Uauy,Cristobal, AU - Borrill,Philippa, AU - Ramírez-González,Ricardo H, AU - De Oliveira,Romain, AU - ,, AU - Mayer,Klaus F X, AU - Paux,Etienne, AU - Choulet,Frédéric, Y1 - 2018/08/17/ PY - 2018/01/25/received PY - 2018/07/11/accepted PY - 2018/8/18/entrez PY - 2018/8/18/pubmed PY - 2018/12/12/medline KW - Genome evolution KW - LTR retrotransposons KW - Polyploidy KW - Transposable elements KW - Triticum aestivum KW - Wheat genome SP - 103 EP - 103 JF - Genome biology JO - Genome Biol. VL - 19 IS - 1 N2 - BACKGROUND: Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS: The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS: Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes. SN - 1474-760X UR - https://www.unboundmedicine.com/medline/citation/30115100/Impact_of_transposable_elements_on_genome_structure_and_evolution_in_bread_wheat_ L2 - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1479-0 DB - PRIME DP - Unbound Medicine ER -