title: Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat.
abstract: Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.
authors.affiliation: Organization and Evolution of Plant Genomes, Unite de Recherche en Genomique Vegetale, Evry Cedex, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Charles
authors.forename: Harry
authors.initials: H
authors.lastname: Belcram
authors.forename: Jérémy
authors.initials: J
authors.lastname: Just
authors.forename: Cécile
authors.initials: C
authors.lastname: Huneau
authors.forename: Agnès
authors.initials: A
authors.lastname: Viollet
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Béatrice
authors.initials: B
authors.lastname: Segurens
authors.forename: Meredith
authors.initials: M
authors.lastname: Carter
authors.forename: Virginie
authors.initials: V
authors.lastname: Huteau
authors.forename: Olivier
authors.initials: O
authors.lastname: Coriton
authors.forename: Rudi
authors.initials: R
authors.lastname: Appels
authors.forename: Sylvie
authors.initials: S
authors.lastname: Samain
authors.forename: Boulos
authors.initials: B
authors.lastname: Chalhoub
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D014908:Triticum / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements
references.citation: Ann Bot. 2005 Jan;95(1):127-32
references.pmid: 15596462
references.citation: Science. 2000 Feb 11;287(5455):1060-2
references.pmid: 10669421
references.citation: Nature. 1993 Nov 18;366(6452):265-8
references.pmid: 8232585
references.citation: Genetics. 2006 Nov;174(3):1493-504
references.pmid: 17028342
references.citation: Plant J. 1998 Dec;16(5):643-50
references.pmid: 10036780
references.citation: Theor Popul Biol. 2002 Jun;61(4):531-44
references.pmid: 12167373
references.citation: Genome Res. 2007 Jul;17(7):1072-81
references.pmid: 17556529
references.citation: Plant Mol Biol. 2000 Jan;42(1):251-69
references.pmid: 10688140
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: J Mol Evol. 1980 Dec;16(2):111-20
references.pmid: 7463489
references.citation: Science. 2002 Apr 5;296(5565):60-3
references.pmid: 11935009
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10
references.pmid: 15240870
references.citation: Nature. 2006 Feb 9;439(7077):749-52
references.pmid: 16467840
references.citation: Genetics. 1971 Jun;68(2):195-211
references.pmid: 17248534
references.citation: Genome. 1999 Apr;42(2):351-60
references.pmid: 10231966
references.citation: BMC Evol Biol. 2007 Aug 29;7:152
references.pmid: 17727727
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Genetica. 2002 May;115(1):29-36
references.pmid: 12188046
references.citation: Tanpakushitsu Kakusan Koso. 2005 Dec;50(16 Suppl):2167-73
references.pmid: 16411447
references.citation: Mol Genet Genomics. 2005 Sep;274(2):119-30
references.pmid: 16034625
references.citation: Genome Res. 2001 Oct;11(10):1660-76
references.pmid: 11591643
references.citation: Nat Genet. 1998 Sep;20(1):43-5
references.pmid: 9731528
references.citation: Curr Opin Plant Biol. 2005 Apr;8(2):135-41
references.pmid: 15752992
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19243-8
references.pmid: 16357197
references.citation: Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227-74
references.pmid: 6977
references.citation: BMC Genomics. 2004 Mar 02;5(1):18
references.pmid: 15040813
references.citation: Chromosome Res. 2007;15(1):21-31
references.pmid: 17295124
references.citation: Genome Res. 2006 Oct;16(10):1262-9
references.pmid: 16963705
references.citation: Funct Integr Genomics. 2002 May;2(1-2):70-80
references.pmid: 12021852
references.citation: Brief Bioinform. 2004 Jun;5(2):150-63
references.pmid: 15260895
references.citation: Plant Physiol. 2005 Dec;139(4):1612-24
references.pmid: 16339807
references.citation: Genetica. 2002 May;115(1):37-47
references.pmid: 12188047
references.citation: Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11844-9
references.pmid: 17615239
references.citation: Plant J. 2005 Jan;41(2):184-94
references.pmid: 15634196
references.citation: BMC Evol Biol. 2006 Aug 16;6:62
references.pmid: 16914031
references.citation: Plant J. 2004 Nov;40(4):500-11
references.pmid: 15500466
references.citation: Proc Natl Acad Sci U S A. 2003 May 13;100(10):6263-8
references.pmid: 12730378
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):383-8
references.pmid: 16381819
references.citation: Plant Cell. 2005 Apr;17(4):1033-45
references.pmid: 15749759
references.citation: Genome Res. 2004 May;14(5):860-9
references.pmid: 15078861
references.citation: Chromosome Res. 2004;12(1):77-91
references.pmid: 14984104
references.citation: Plant Cell. 2000 Jul;12(7):1093-101
references.pmid: 10899976
references.citation: Mol Biol Evol. 2008 Jul;25(7):1415-28
references.pmid: 18400789
references.citation: Genome Biol. 2004;5(10):R79
references.pmid: 15461797
references.citation: Genome Biol. 2002;3(12):RESEARCH0084
references.pmid: 12537573
references.citation: Plant Cell. 1997 Sep;9(9):1509-1514
references.pmid: 12237393
references.citation: Plant Physiol. 2003 May;132(1):52-63
references.pmid: 12746511
references.citation: Funct Integr Genomics. 2003 Mar;3(1-2):39-55
references.pmid: 12590342
references.citation: Plant J. 2006 Nov;48(3):463-74
references.pmid: 17010109
references.citation: Plant Cell. 2000 Jul;12(7):1021-9
references.pmid: 10899971
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17638-43
references.pmid: 17101966
references.citation: Ann Bot. 2005 Jan;95(1):1-6
references.pmid: 15596455
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9691-6
references.pmid: 18599450
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Plant Cell. 1999 Sep;11(9):1769-1784
references.pmid: 10488242
references.citation: Genome Res. 2005 Apr;15(4):526-36
references.pmid: 15805493
references.citation: Plant Cell. 2003 May;15(5):1186-97
references.pmid: 12724543
references.citation: Genome Res. 2002 Jul;12(7):1075-9
references.pmid: 12097344
references.citation: Mol Genet Genomics. 2006 Feb;275(2):193-203
references.pmid: 16362370
references.citation: Bioinformatics. 2000 Oct;16(10):944-5
references.pmid: 11120685
references.citation: Genetica. 2002 May;115(1):81-91
references.pmid: 12188050
references.citation: Mol Genet Genomics. 2002 Dec;268(4):488-99
references.pmid: 12471446
references.citation: Nat Genet. 2003 Jan;33(1):102-6
references.pmid: 12483211
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8
references.pmid: 15161969
references.citation: Genome Res. 2006 Oct;16(10):1252-61
references.pmid: 16954538
references.citation: Cytogenet Genome Res. 2005;109(1-3):250-8
references.pmid: 15753584
references.citation: Plant Cell. 2008 Jan;20(1):11-24
references.pmid: 18178768
references.citation: Science. 1996 Nov 1;274(5288):765-8
references.pmid: 8864112
references.citation: Plant Physiol. 2008 Jan;146(1):45-59
references.pmid: 18032588
references.citation: Nat Rev Genet. 2007 Dec;8(12):973-82
references.pmid: 17984973
references.citation: Theor Appl Genet. 1990 Dec;80(6):826-32
references.pmid: 24221117
references.citation: Genome. 1993 Feb;36(1):21-31
references.pmid: 18469969
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Mol Biol Evol. 2006 Jul;23(7):1386-96
references.pmid: 16675504
references.citation: Plant J. 2004 Sep;39(6):960-8
references.pmid: 15341637
references.citation: Genetica. 2002 May;115(1):49-63
references.pmid: 12188048
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8133-8
references.pmid: 12060759