Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids

Genome

Volumn 49, Issue 8, 2006, Pages 1023-1035

  Salina, Elena A ^a   Lim, K Yoong ^b   Badaeva, Ekaterina D ^c   Shcherban, Andrey B ^a   Adonina, Irina G ^a   Amosova, Alexandra V ^c   Samatadze, Tatiana E ^c   Vatolina, Tatyana Yu ^a   Zoshchuk, Sviatoslav A ^c   Leitch, Andrew R ^b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

Aegilops; B and G genome; Evolution; RAPD; Subtelomeric tandem repeats; Wheat

Indexed keywords

PLANT DNA; PRIMER DNA;

ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; DIPLOIDY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE DOSAGE; GENETICS; GENOME; KARYOTYPING; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POACEAE; POLYPLOIDY; RANDOM AMPLIFIED POLYMORPHIC DNA; SPECIES DIFFERENCE; TANDEM REPEAT; WHEAT;

BASE SEQUENCE; DIPLOIDY; DNA PRIMERS; DNA, PLANT; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; GENE DOSAGE; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; PHYLOGENY; POACEAE; POLYPLOIDY; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; SPECIES SPECIFICITY; TANDEM REPEAT SEQUENCES; TRITICUM;

AEGILOPS; TRITICUM; TRITICUM AESTIVUM; TRITICUM TIMOPHEEVII;

EID: 33845393914     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G06-050     Document Type: Article

References (83)

1. Ankory, H., and Zohary, D. 1962. Natural hybridization between Aegilops sharonensis and Ae. longissima: a morphological and cytological study. Cytologia, 27: 314-324.
2. Adonina, I.G., Salina, E.A., Efremova, T.T., and Pshenichnikova, T.A. 2004. The study of introgressive lines of Triticum aestivum x Aegilops speltoides by in situ and SSR analyses. Plant Breed. 123: 220-224.
3. Adonina, I.G., Salina, E.A., Pestsova, E.G., and Röder, M.S. 2005. Transferability of wheat microsatellites to diploid Aegilops species and determination of chromosomal localizations of microsatellites in the S genome. Genome, 48: 959-970.
4. Anamthawat-Jonsson, K., and Heslop-Harrison, J.S. 1993. Isolation and characterization of genome-specific DNA sequences in Triticeae species. Mol. Gen. Genet. 240: 151-158.
5. Appels, R., Moran, L.B., and Gustafson, J.P. 1986. Rye heterochromatin I. Studies on clusters of the major repeating sequences and the identification of a new dispersed repetitive sequences element. Can. J. Genet. Cytol. 28: 645-657.
6. Badaeva, E.D., Budashkina, E.B., Badaev, N.S., Kalinina, N.P., and Shkutina, F.M. 1991. General features of chromosome substitutions in Triticum aestivum x T. timopkeevii hybrids. Theor. Appl. Genet. 82: 227-232.
7. Badaeva, E.D. 2000. Chromosome analysis in investigation of the origin of the B- and G-genomes of polyploid wheats. Membr. Cell Biol. 18: 216-229. [In Russian.]
8. Badaeva, E.D., Badaev, N.S., Gill B.S., and Filatenko, A.A. 1994. Intraspecific karyotype divergence in Triticum araraticum. Plant Syst. Evol. 192: 117-145.
9. Badaeva, E.D., Friebe, B., and Gill, B.S. 1996a. Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species. Genome, 39: 293-306.
10. Badaeva, E.D., Friebe, B., and Gill B.S. 1996b. Genome differentiation in Aegilops. 1. Physical mapping of 5S and 18S-26S ribosomal RNA gene families in diploid species. Genome, 39: 1150-1158.
11. Bass, H.W. 2003. Telomere dynamics unique to meiotic prophase: formation and significance of the bouquet. Cell. Mol. Life Sci. 60: 2319-2324.
12. Bedbrook, R.J., Jones, J., O'Dell, M., Thompson, R.J., and Flavell, R.B. 1980. A molecular description of telomeric beterochromatin in Secale species. Cell, 19: 545-560.
13. Bildanova, L.L., Salina E.A., and Pershina, L.A. 2002. Investigation of the backcross progeny of barley-wheat hybrids by the RAPD and RAMPO methods. Rus. J. Gen. 38: 257-263.
14. Chen, P.D., and Gill, B.S. 1983. The origin of chromosome 4A. and genomes B and G of tetraploid wheats. In Proceedings of the 6th International Wheat Genetics Symposium, Kyoto, Japan. Edited by S. Sakamoto. pp. 39-48.
15. Contento, A., Heslop-Harrison, J.S., and Schwarzacher T. 2005. Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae. Cytogenet. Genome Res. 109: 34-42.
16. Cowan, C.R., Carlton, P.M., and Cande, W.Z. 2001. The polar arrangement of telomeres in interphase and meiosis. Rab1 organization and the bouquet. Plant Physiol. 125: 532-538.
17. Dvorak, J., and Appels, R. 1982. Chromosome and nucleotide sequence differentiation in genomes of polyploid Triticum species. Theor. Appl. Genet. 63: 349-360.
18. Dvorak, J., and Zhang, H.-B. 1992. Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences. Theor. Appl. Genet. 84: 419-429.
19. Dvorak, J., Mcguire, P.E., and Cassidy, B. 1988. Apparent sources of the A genomes of wheats inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome, 30: 680-689.
20. Eig. A. 1929. Monographisch-kritische Ubersicht der Gattung Aegilops. Repertorium Specierum Novarum Regni Vegetabilis, 55: 1-228.
21. Feldman, M., Lupton, F.G.H., and Miller, T.E. 1995. Wheats. In Evolution of crop plants. Edited by J. Smartt and N.W. Simmonds. Longman Group, London, U.K. pp. 184-192.
22. Feldman, M. 2001. Origin of cultivated wheat. In The world wheat book. Edited by A.P. Bonjean and W.J. Angus. Lavoisier Publishing, Paris, France, pp. 3-56.
23. Felsenstein, J. 1989. PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics, 5: 164-166.
24. Flavell, R.B. 1982. Amplification, deletion and rearrangement: major sources of variation during species divergence. In Genome evolution. Edited by G.A. Dover and R.B. Flavell. Academic Press, London.
25. Friebe, B., and Gill, B.S. 1996. Chromosome banding and genome analysis in diploid and cultivated polyploid wheats. In Methods of genome analysis in plants. Edited by P.P. Jauhar. CRC Press, New York. pp. 39-60.
26. Friebe, B., Tuleen, N., Jiang, J., and Gill, B.S. 1993. Standard karyotype of Triticum longissimum and its cytogenetic relationship with T. aestivum. Genome, 36: 731-742.
27. Friebe, B., Qi, L.L., Nasuda, S., Zhang, P., Tuleen, N.A., and Gill, B.S. 2000. Development of a complete set of Triticum aestivum-Aegilops speltoides chromosome addition lines. Theor. Appl. Genet. 101: 51-58.
28. Gill, B.S., and Friebe, B. 1998. Plant cytogenetics at the dawn of the 21st century. Curr. Opin. Plant Biol. 1: 109-115.
29. Gill, B.S., Friebe, B., and Endo, T.R. 1991. Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome, 34: 830-839.
30. Giorgi, D., D'ovidio, R., Tanzarella, O.A., and Porceddu, E. 2002. RFLP analysis of Aegilops species belonging to the Sitopsis section. Genet. Resour. Crop Evol. 49: 145-151.
31. Heslop-Harrison, J.S. 2000. Comparative genome organization in plants: from sequences and markers to chromatin and chromosome. Plant Cell, 12: 617-635.
32. Huang, S., Sirikhachornkit, A., Su, X., Faris, J., Gill, B., Haselkorn, R., and Gornicki, P. 2002. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticuml Aegilops complex and the evolutionary history of polyploids wheat. Proc. Natl. Acad. Sci. U.S.A. 99: 8133-8138.
33. Jiang, J., and Gill, B.S. 1994. Different species-specific chromosome translocation in Triticum timopheevii and T. turgidum support diphyletic origin of polyploid wheats. Chromosome Res. 2: 59-64.
34. Jones, J.D.G., and Flavell, R.B. 1982. The structure, amount and chromosomal localization of defined repeated DNA sequences in species of the genus Secale. Chromosoma, 86: 613-641.
35. Katsiotis, A., Hagidimitriou, M., and Heslop-Harrison, J.S. 1997. The close relationship between the A and B genomes in Avena L. (Poaceae) determined by molecular cytogenetic analysis of total genomic, tandemly and dispersed repetitive DNA. Ann. Bot. 79: 103-107.
36. Kerby, K., and Kuspira, J. 1987. The phylogeny of the polyploid wheats Triticum aestivum (bread wheat) and Triticum turgidum (macaroni wheat). Genome, 29: 722-737.
37. Khlestkina, E.K., and Salina, E.A. 2001. Genome-specific markers of tetraploid wheats and their putative diploid progenitor species. Plant Breed. 120: 227-232.
38. Kishii, M., and Tsujimoto, H. 2002. Genus-specific localization of the Tail family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat. Genome, 45: 946-955.
39. Kilian, A., and Kleinhofs, A. 1992. Cloning and mapping of telomere-associated sequences from Hordeum vulgare L. Mol. Gen. Genet. 235: 153-156.
40. Kumar, S., Tamura K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Arizona State University, U.S.A.
41. Lagercrantz, U., and Lydiate, D.J. 1996. Comparative genome mapping in Brassica. Genetics, 144: 1903-1910.
42. Leitch, J.J., and Bennett, M.D. 1997. Polyploidy in angiosperms. Trends Plant Sci. 2: 470-476.
43. Leitch, A.R., Schwarzacher, T., Jackson, D., and Leitch, I.J. 1994. In situ hybridization: a practical guide. BIOS, Oxford.
44. Levy, A. V., and Feldman, M. 2002. The impact of polyploidy on grass genome evolution. Plant Physiol. 130: 1587-1593.
45. Lilienfeld, F., and Kihara, H. 1934. Genomanalyze bei Triticum und Aegilops. V. Triticum timopheevi Zhuk. Cytologia, 6: 87-122.
46. Lim, K.Y., Matyasek, R., Lichtenstein, C.P., and Leitch, A.R. 2000. Molecular cytogenetic analyses and phylogeny of the Nicotiana section Tomentosae. Chromosoma, 109: 245-258.
47. Liu, B., and Wendel, J.F. 2003. Epigenetic phenomena and the evolution of plant allopolyploids. Mol. Phylogenet. Evol. 29: 365-379.
48. Liu, C.J., Atkinson, M.D., Chinoy, C.N., Devos, K.M., and Gale M.D. 1992. Nonhomoeologous translocations between group 4, 5 and 7 chromosomes within wheat and rye. Theor. Appl. Genet. 83: 305-312.
49. Maestra, B., and Naranjo, T. 1999. Structural chromosome differentiation between Triticum timopheevii and T. turgidum and T. aestivum. Theor. Appl. Genet. 98: 744-750.
50. McIntyre, C.L., Pereira, S., Moran, L.B., and Appels, R. 1990. New secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat. Genome, 33: 635-640.
51. Mori, N., Lui, Y.G., and Tsunewaki, K. 1995. Wheat phylogeny determined by RFLP analysis of nuclear DNA: II. Wild tetraploid wheats. Theor. Appl. Genet. 90: 129-134.
52. Mukai, Y., Nakahara, Y., and Yamamoto, M. 1993. Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome, 36: 489-494.
53. Nagaki, K., Tsujimoto, H., Isono, K., and Sasakuma, T. 1995. Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae. Genome, 38: 479-486.
54. Nagaki, K., Tsujimoto, H., and Sasakuma, T. 1998. H genome specific repetitive sequence, pEt2, of Elymus trachycaulus in part of Afa family of Triticeae. Genome, 41: 134-136.
55. Naranjo, T., Roca, A., Goicoecha, P.O., and Giraldez, R. 1987. Arm homoeology of wheat and rye chromosomes. Genome, 29: 873-882.
56. Nei, M., and Li, W.H. 1979. Mathematical model for studing genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A. 76: 5269-5273.
57. Pestsova, E.G., Goncharov, N.P., and Salina, E.A. 1998. Elimination of a tandem repeat of telomeric heterochromatin during evolution of wheat. Theor. Appl. Genet. 97: 1380-1386.
58. Polanco, C., Gonzalez, A.I., de la Fuente, A., and Dover, G.A. 1998. Multigene family of ribosomal DNA in Drosophila melanogaster reveals contrasting patterns of homogenization for IGS and ITS spacer regions: a possible mechanism to resolve this paradox. Genetics, 149: 243-256.
59. Rayburn, A.L., and Gill, B.S. 1986. Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant. Mol. Biol. Rep. 4: 102-109.
60. Rieseberg, L.H. 2001. Polyploid evolution: keeping the peace at genomic reunions. Curr. Biol. 11: R925-R928.
61. Salina, E.A., Pestsova, E.G., Adonina, I.G., and Vershinin, A.V. 1998. Identification of a new family of tandem repeats in Triticeae genomes. Euphytica, 100: 231-237.
62. Salina, E., Adonina, I., Vatolina, T., and Kurata, N. 2004a. A comparative analysis of the composition and organization of two subtelomeric repeat families in Aegilops speltoides Tausch., and related species. Genetica, 122: 227-237.
63. Salina, E.A., Numerova, O.M., Ozkan, H., and Feldman, M. 2004b. Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat. Genome, 47: 860-867.
64. Salina, E.A., Leonova, I.N., Efremova, T.T., and Röder, M.S. 2005. Wheat genome structure: translocations during the course of polyploidization. Funct. Integr. Genomics: doi:10.1007/s10142-005-0001-4.
65. Salina, E.A., Leonova, I.N., Efremova, T.T., and Röder, M.S. 2006. Wheat genome structure: translocations during the course of polyploidization. Funct. Integr. Genomics, 6: 71-80.
66. Sasanuma, T., Miyashita, N.T., and Tsunewaki, K. 1996. Wheat phylogeny determined by RFLP analysis of nuclear DNA. 3. Intra- and interspecific variations of five Aegilops Sitopsis species. Theor. Appl. Genet. 92: 928-934.
67. Schmidt, T., and Heslop-Harrison, J.S. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci. 3: 195-199.
68. Sharma, S., and Raina, S.N. 2005. Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet. Genome Res. 109: 15-26.
69. Schlotterer, C., and Tautz, D. 1994. Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Curr. Biol. 4: 777-783.
70. Soltis, D.E., and Soltis, P.S. 1995. The dynamic nature of polyploid genomes. Proc. Nat. Acad. Sci. U.S.A. 92: 8089-8091.
71. Soltis, D.E., and Soltis, P.S. 1999. Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14: 348-352.
72. Soltis, D.E., Soltis, P.S., and Tate, J.A. 2004. Advances in the study of polyploidy since Plant speciation. New Phytol. 161: 173-191.
73. Taketa, S., Ando H., Takeda K., Harrison G.E., and Heslop-Harrison J.S. 2000. The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in the genus Hordeum. Theor. Appl. Genet. 100: 169-176.
74. Tanaka, M. 1955. Chromosome pairing in hybrids between Ae. sharonensis and some species of Aegilops and Triticum. Wheat Information Service, 2: 7-10.
75. Trifonov, E.N. 1985. Curved DNA. CRC Crit. Rev. Biochem. 19: 89-106.
76. Tsunewaki, K. 1996. Plasmon analysis as the counterpart of genome analysis. In Methods of genome analysis in plants. Edited by P.P. Jauhar. CRC Press, New York. pp. 271-299.
77. Vershinin, A.V., and Heslop-Harrison, J.S. 1998. Comparative analysis of the nucleosomal structure of rye, wheat and their relatives. Plant Mol. Biol. 36: 149-161.
78. Vershinin, A.V., Svitashev, S., Gummesson, P.-O., Salomon, B., Bothmer, R., and Bryngelsson, T. 1994. Characterization of a family of tandemly repeated DNA sequences in Triticeae. Theor. Appl. Genet. 89: 217-225.
79. Vershinin, A.V., Schwarzacher, T., and Heslop-Harrison, J.S. 1995. The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosome. Plant Cell, 7: 1823-1833.
80. Vershinin, A.V., Alkhimova, E.G., and Heslop-Harrison, J.S. 1996. Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species. Chromosome Res. 4: 515-525.
81. Wendel, J.F. 2000. Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
82. Zhang, P., Friebe, B., and Gill, B.S. 2002. Variation in the distribution of a genome-specific DNA sequences on chromosomes reveals evolutionary relations in the Triticum and Aegilops complex. Plant Syst. Evol. 235: 169-179.
83. Zhang, H., Reader, S.M., Lui, X., Jia, J.Z., Gale, M.D., and Devos, K.M. 2001. Comparative genetic analysis of the Aegilops longissima and Ae. sharonensis genomes with common wheat. Theor. Appl. Genet. 103: 518-525.