The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Salina, Elena A ^a   Sergeeva, Ekaterina M ^a   Adonina, Irina G ^a   Shcherban, Andrey B ^a   Belcram, Harry ^b   Huneau, Cecile ^b   Chalhoub, Boulos ^b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AEGILOPS SPELTOIDES; EUKARYOTA; TRITICUM AESTIVUM;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLASSIFICATION; DIPLOIDY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LIBRARY; GENE TRANSLOCATION; GENETICS; METAPHASE; MOLECULAR EVOLUTION; PHYLOGENY; PLANT CHROMOSOME; PLANT GENE; PLANT GENOME; POLYPLOIDY; RETROPOSON; WHEAT;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DIPLOIDY; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; GENOMIC LIBRARY; IN SITU HYBRIDIZATION, FLUORESCENCE; METAPHASE; PHYLOGENY; POLYPLOIDY; RETROELEMENTS; TRANSLOCATION, GENETIC; TRITICUM;

EID: 79957790638     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-99     Document Type: Article

References (58)

1. Von Sternberg RM, Novick GE, Gao GP, Herrera RJ. Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA. Transposable Elements and Evolution 1992, 108-139. Dordrecht: Kluwer Academic Publishers, McDonald JF.
2. Charlesworth B, Sniegowski P, Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 1994, 371:215-220. 10.1038/371215a0, 8078581.
3. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, Wing RA. Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 2004, 101:14349-14354. 10.1073/pnas.0406163101, 521949, 15388850.
4. International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project.
5. Sabot F, Guyot R, Wicker T, Chantret N, Laubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics 2005, 274:119-130. 10.1007/s00438-005-0012-9, 16034625.
6. Charles M, Belcram H, Just J, Huneau C, Viollet A, Couloux A, Segurens B, Carter M, Huteau V, Coriton O, Appels R, Samain S, Chalhoub B. Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 2008, 180:1071-1086. 10.1534/genetics.108.092304, 2567357, 18780739.
7. Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 2006, 48:463-474. 10.1111/j.1365-313X.2006.02891.x, 17010109.
8. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 2010, 22(6):1686-701. 10.1105/tpc.110.074187, 2910976, 20581307.
9. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8:973-982. 10.1038/nrg2165, 17984973.
10. Casacuberta JM, Santiago N. Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 2003, 311:1-11.
11. Bennett MD, Leitch IJ. Nuclear DNA amounts in Angiosperms. Ann Bot 1995, 76:113-176.
12. Bennetzen JL. The evolution of grass genome organisation and function. Symp Soc Exp Biol 1998, 51:123-126.
13. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O. Doubling genome size without polyploidization: dynamics of retrotransposition driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 2006, 16:1262-1269. 10.1101/gr.5290206, 1581435, 16963705.
14. Le HT, Armstrong RC, Miki B. Detection of rye DNA in wheat-rye hybrids and wheat translocation stocks using total genomic DNA as a probe. Plant Mol Biol Rep 1989, 7:150-158.
15. Schwarzacher T, Anamthawat-Jónsson K, Harrison GE, Islam AKMR, Jia JZ, King IP, Leitch AR, Miller TE, Reader SM, Rogers WJ, Shi M, Heslop-Harrison JS. Genomic in situ hybridization to identify alien chromosomes and chromosome segments in wheat. Theor Appl Genet 1992, 84:778-786.
16. Mukai Y, Nakahara Y, Yamamoto M. Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 1993, 36:489-494. 10.1139/g93-067, 18470003.
17. Mestiri I, Chagué V, Tanguy AM, Huneau C, Huteau V, Belcram H, Coriton O, Chalhoub B, Jahier J. Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol 2010, 186(1):86-101. 10.1111/j.1469-8137.2010.03186.x, 20149116.
18. Feldman M, Lupton FGH, Miller TE. Wheats. Evolution of crops 1995, 184-192. London: Longman Scientific, Smartt J, Simmonds NW.
19. Blake NK, Lehfeldt BR, Lavin M, Talbert LE. Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: the B genome of wheat. Genome 1999, 42:351-360. 10.1139/g98-136, 10231966.
20. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 2002, 99:8133-8138. 10.1073/pnas.072223799, 123033, 12060759.
21. Dvorak J, Akhunov ED, Akhunov AR, Deal KR, Luo MC. Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat. Mol Biol Evol 2006, 23:1386-1396. 10.1093/molbev/msl004, 16675504.
22. Belyayev A, Raskina O, Nevo E. Detection of alien chromosomes from S-genome species in the addition/substitution lines of bread wheat and visualization of A-, B- and D-genomes by GISH. Hereditas 2001, 135(2-3):119-22.
23. Belyayev A, Raskina O, Korol A, Nevo E. Coevolution of A and B genomes in allotetraploid Triticum dicoccoides. Genome 2000, 43(6):1021-6.
24. Zhang P, Li W, Friebe B, Gill BS. Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH. Genome 2004, 47(5):979-87. 10.1139/g04-042, 15499412.
25. Pedersen C, Langridge P. Identification of the entire chromosome complement of bread wheat by two-colour FISH. Genome 1997, 40(5):589-93. 10.1139/g97-077, 18464850.
26. Salina EA, Lim KY, Badaeva ED, Shcherban AB, Adonina IG, Amosova AV, Samatadze TE, Vatolina TY, Zoshchuk SA, Leitch AR. Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome 2006, 49:1023-1035. 10.1139/G06-050, 17036077.
27. Raskina O, Belyayev A, Nevo E. Repetitive DNAs of wild emmer wheat (Triticum dicoccoides) and their relation to S-genome species: molecular cytogenetic analysis. Genome 2002, 45:391-401. 10.1139/g01-142, 11962636.
28. Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B. Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 2005, 17:1033-1045. 10.1105/tpc.104.029181, 1087984, 15749759.
29. Gu YQ, Salse J, Coleman-Derr D, Dupin A, Crossman C, Lazo GR, Huo N, Belcram H, Ravel C, Charmet G, Charles M, Anderson OD, Chalhoub B. Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics 2006, 174:1493-1504. 10.1534/genetics.106.060756, 1667099, 17028342.
30. Chalupska D, Lee HY, Faris JD, Evrard A, Chalhoub B, Haselkorn R, Gornicki PL. Acc homoeoloci and the evolution of wheat genomes. Proc Natl Acad Sci USA 2008, 105:9691-9696. 10.1073/pnas.0803981105, 2474508, 18599450.
31. Salse J, Chagué V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A, Segurens B, Charles M, Ravel C, Samain S, Charmet G, Boudet N, Chalhoub B. New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics 2008, 9:555. 10.1186/1471-2164-9-555, 2612700, 19032732.
32. Isidore E, Scherrer B, Chalhoub B, Feuillet C, Keller B. Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Research 2005, 15:526-536. 10.1101/gr.3131005, 1074367, 15805493.
33. Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B. Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell 2003, 15(5):1186-97. 10.1105/tpc.011023, 153725, 12724543.
34. Dubcovsky J, Dvorak J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 2007, 316(5833):1862-6. 10.1126/science.1143986, 17600208.
35. Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B. Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics 2009, 10:414. 10.1186/1471-2164-10-414, 2756281, 19732459.
36. Schneider A, Linc G, Molnár-Láng M, Graner A. Fluorescence in situ hybridization polymorphism using two repetitive DNA clones in different cultivars of wheat. Plant Breeding 2003, 122:396-400.
37. Naranjo T, Roca A, Goicoechea PG, Giraldez R. Arm homoeology of wheat and rye chromosomes. Genome 1987, 29:873-882.
38. Devos KM, Dubcovsky J, Dvorák J, Chinoy CN, Gale MD. Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination. Theor Appl Genet 1995, 91:282-288.
39. Sergeeva EM, Salina EA, Adonina IG, Chalhoub B. Analysis of CACTA DNAtransposon Caspar evolution across wheat species by sequence comparison and in situ hybridization. Mol Genet Genomics 2010, 284(1):11-23. 10.1007/s00438-010-0544-5, 20512353.
40. Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 2010, 8(2):196-210. 10.1111/j.1467-7652.2009.00477.x, 20078842.
41. Ahn S, Anderson JA, Sorrels ME, Tanksley SD. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 1993, 241:483-490. 10.1007/BF00279889, 7903411.
42. Wicker T, Matthews DE, Keller B. TREP: A database for Triticeae repetitive elements. Trends Plant Sci 2002, 7:561-562., http://wheat.pw.usda.gov/ITMI/Repeats
43. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
44. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunesekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucl Acids Res 2010, 38:D211-222. 10.1093/nar/gkp985, 2808889, 19920124.
45. National Center for Biotechnology Information Nucleotide database. , http://www.ncbi.nlm.nih.gov/nuccore
46. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
47. Fuchs J, Houben A, Brandes A, Schubert I. Chromosome 'painting' in plants - a feasible technique?. Chromosoma 1996, 104:315-320.
48. Heslop Harrison JS, Schwarzacher T. Genomic Southern and In Situ hybridization for plant genome analysis. Methods of Genome Analysis in Plants 1996, 163-179. Boca Raton, NY: CRC Press, Jauhar PP.
49. Lim KY, Kovarik A, Matyasek R, Chase MW, Clarkson JJ, Grandbastien MA, Leitch AR. Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years. New Phytol 2007, 175:756-763. 10.1111/j.1469-8137.2007.02121.x, 17688590.
50. Zhang P, Li W, Fellers J, Friebe B, Gill BS. BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 2004, 112:288-299. 10.1007/s00412-004-0273-9, 14986017.
51. Gill BS, Kimber G. Giemsa C-banding and the evolution of wheat. Proc Natl Acad Sci USA 1974, 71:4086-4090. 10.1073/pnas.71.10.4086, 434333, 16592188.
52. Badaeva ED, Friebe B, Gill BS. Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosome of diploid species. Genome 1996, 39(2):293-306. 10.1139/g96-040, 18469894.
53. Maniatis T, Fritsch EF, Sambrook J. Molecular cloning 1982, Cold Spring Harbor: Cold Spring Harbor Lab.
54. Feinberg AP, Vogelstein BA. A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 1983, 132:6-13. 10.1016/0003-2697(83)90418-9, 6312838.
55. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
56. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
57. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet 1998, 20:43-45. 10.1038/1695, 9731528.
58. Ma J, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 2004, 101:12404-12410. 10.1073/pnas.0403715101, 515075, 15240870.