Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat.
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.
Charles
Mathieu
M
Organization and Evolution of Plant Genomes, Unite de Recherche en Genomique Vegetale, Evry Cedex, France.
Belcram
Harry
H
Just
Jérémy
J
Huneau
Cécile
C
Viollet
Agnès
A
Couloux
Arnaud
A
Segurens
Béatrice
B
Carter
Meredith
M
Huteau
Virginie
V
Coriton
Olivier
O
Appels
Rudi
R
Samain
Sylvie
S
Chalhoub
Boulos
B
D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D014908:Triticum / Q000235:genetics*
D004251:DNA Transposable Elements
Ann Bot. 2005 Jan;95(1):127-32
15596462
Science. 2000 Feb 11;287(5455):1060-2
10669421
Nature. 1993 Nov 18;366(6452):265-8
8232585
Genetics. 2006 Nov;174(3):1493-504
17028342
Plant J. 1998 Dec;16(5):643-50
10036780
Theor Popul Biol. 2002 Jun;61(4):531-44
12167373
Genome Res. 2007 Jul;17(7):1072-81
17556529
Plant Mol Biol. 2000 Jan;42(1):251-69
10688140
Nature. 2007 Sep 27;449(7161):463-7
17721507
J Mol Evol. 1980 Dec;16(2):111-20
7463489
Science. 2002 Apr 5;296(5565):60-3
11935009
Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10
15240870
Nature. 2006 Feb 9;439(7077):749-52
16467840
Genetics. 1971 Jun;68(2):195-211
17248534
Genome. 1999 Apr;42(2):351-60
10231966
BMC Evol Biol. 2007 Aug 29;7:152
17727727
Methods Mol Biol. 2000;132:365-86
10547847
Genetica. 2002 May;115(1):29-36
12188046
Tanpakushitsu Kakusan Koso. 2005 Dec;50(16 Suppl):2167-73
16411447
Mol Genet Genomics. 2005 Sep;274(2):119-30
16034625
Genome Res. 2001 Oct;11(10):1660-76
11591643
Nat Genet. 1998 Sep;20(1):43-5
9731528
Curr Opin Plant Biol. 2005 Apr;8(2):135-41
15752992
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19243-8
16357197
Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227-74
6977
BMC Genomics. 2004 Mar 02;5(1):18
15040813
Chromosome Res. 2007;15(1):21-31
17295124
Genome Res. 2006 Oct;16(10):1262-9
16963705
Funct Integr Genomics. 2002 May;2(1-2):70-80
12021852
Brief Bioinform. 2004 Jun;5(2):150-63
15260895
Plant Physiol. 2005 Dec;139(4):1612-24
16339807
Genetica. 2002 May;115(1):37-47
12188047
Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11844-9
17615239
Plant J. 2005 Jan;41(2):184-94
15634196
BMC Evol Biol. 2006 Aug 16;6:62
16914031
Plant J. 2004 Nov;40(4):500-11
15500466
Proc Natl Acad Sci U S A. 2003 May 13;100(10):6263-8
12730378
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):383-8
16381819
Plant Cell. 2005 Apr;17(4):1033-45
15749759
Genome Res. 2004 May;14(5):860-9
15078861
Chromosome Res. 2004;12(1):77-91
14984104
Plant Cell. 2000 Jul;12(7):1093-101
10899976
Mol Biol Evol. 2008 Jul;25(7):1415-28
18400789
Genome Biol. 2004;5(10):R79
15461797
Genome Biol. 2002;3(12):RESEARCH0084
12537573
Plant Cell. 1997 Sep;9(9):1509-1514
12237393
Plant Physiol. 2003 May;132(1):52-63
12746511
Funct Integr Genomics. 2003 Mar;3(1-2):39-55
12590342
Plant J. 2006 Nov;48(3):463-74
17010109
Plant Cell. 2000 Jul;12(7):1021-9
10899971
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17638-43
17101966
Ann Bot. 2005 Jan;95(1):1-6
15596455
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9691-6
18599450
Nature. 2001 Feb 15;409(6822):860-921
11237011
Plant Cell. 1999 Sep;11(9):1769-1784
10488242
Genome Res. 2005 Apr;15(4):526-36
15805493
Plant Cell. 2003 May;15(5):1186-97
12724543
Genome Res. 2002 Jul;12(7):1075-9
12097344
Mol Genet Genomics. 2006 Feb;275(2):193-203
16362370
Bioinformatics. 2000 Oct;16(10):944-5
11120685
Genetica. 2002 May;115(1):81-91
12188050
Mol Genet Genomics. 2002 Dec;268(4):488-99
12471446
Nat Genet. 2003 Jan;33(1):102-6
12483211
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8
15161969
Genome Res. 2006 Oct;16(10):1252-61
16954538
Cytogenet Genome Res. 2005;109(1-3):250-8
15753584
Plant Cell. 2008 Jan;20(1):11-24
18178768
Science. 1996 Nov 1;274(5288):765-8
8864112
Plant Physiol. 2008 Jan;146(1):45-59
18032588
Nat Rev Genet. 2007 Dec;8(12):973-82
17984973
Theor Appl Genet. 1990 Dec;80(6):826-32
24221117
Genome. 1993 Feb;36(1):21-31
18469969
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Mol Biol Evol. 2006 Jul;23(7):1386-96
16675504
Plant J. 2004 Sep;39(6):960-8
15341637
Genetica. 2002 May;115(1):49-63
12188048
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8133-8
12060759