ПОВТОРЯЮЩИЕСЯ ПОСЛЕДОВАТЕЛЬНОСТИ ДНК В ГЕНОМАХ РАСТЕНИЙ
Аннотация
Обзор посвящен характеристике основных классов повторяющихся последовательностей ДНК, включая кодирующие (гены рРНК) и некодирующие последовательности (тандемные и диспергированные повторы). Обсуждается особая роль этих компонентов в формировании структурно-функциональной организации генома высших растений, а также в обеспечении повышенной по сравнению с геномом животных генетической изменчивости на уровне как отдельных последовательностей, так и генома.
Ключевые слова
высшие растения,
повторяющиеся последовательности ДНК,
гены рРНК,
тандемный повтор,
мобильный элемент
При поддержке: проект по фундаментальным научным исследованиям (тема № VI.53.1.5.), грант РФФИ № 14-04-00297
Об авторе
А. Б. Щербань
Федеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, Россия
Россия
Россия
Список литературы
1. Сергеева Е.М., Салина Е.А. Мобильные элементы и эволюция генома растений // Вавилов. журн. генет. и селекции. 2011. Т. 15. № 2. С. 382–397.
2. Хемлебенб В., Беридзе Т.Г., Бахман Л., Коварик Я., Торрес Р. Сателлитные ДНК // Усп. биол. химии. 2003. Т. 43. С. 267–306.
3. Alkhimova O.G., Mazurok N.A., Potapova T.A., Zakian S.M. et al. Diverse patterns of the tandem repeats organization in rye chromosomes // Chromosoma. 2004. V. 113. P. 42–52.
4. Anamthawat-Josson K., Heslop-Harrison J.S. Isolation and characterization of genome-specifi c DNA sequences in Triticeae species // Mol. Gen. Genet. 1993. V. 240. P. 151–158.
5. Ananiev E.V., Phillips R.L., Rines H.W. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions // Proc. Natl Acad. Sci. USA. 1998. V. 95. P. 13073–13078.
6. Appels R., Baum B.R., Clarke B.C. The 5S DNA units of bread wheat (Triticum aestivum L.) // Plant Syst. Evol. 1992. V. 183. P. 183–194.
7. Appels R., Dvořák J. Relative rates of divergence of spacer and gene sequences within the rDNA region of species in the Triticeae: Implications for the maintenance of homogeneity of a repeated gene family // Theor. Appl. Genet. 1982a. V. 63. P. 361–365.
8. Appels R., Dvořák J. The wheat ribosomal DNA spacer region: Its structure and variation in populations and among species // Theor. Appl. Genet. 1982b. V. 63. P. 337–348.
9. Appels R., Gerlach W.L., Dennis E.S. et al. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals // Chromosoma. 1980. V. 78. P. 293–311.
10. Bedbrook J.H., Jones J., O’Del M. A molecular distribution of telomeric heterochromatin in Secale species // Cell. 1980. V. 19. P. 545–560.
11. Belo A., Beatty M., Hondred D., Fengler K. et al. Allelic genome structural variations in maize detected by array comparative genome hybridization // Theor. Appl. Genet. 2010. V. 120. P. 355–367.
12. Bennett M., Leitch I.J. Nuclear DNA amounts in angiosperms: targets, trends and tomorrow // Ann. Bot. 2011. V. 107. P. 467–590.
13. Bennetzen J.L. The contribution of retroelements to plant genome organization, function and evolution // Trends Microbiol. 1996. V. 4. P. 347–353.
14. Biemont C. Genome size evolution: within-species variation in genome size // Heredity. 2008. V. 101. P. 297–298.
15. Bureau T.E., Wessler S.R. Tourist: a large family of invertedrepeat elements frequently associated with maize genes // Plant Cell. 1992. V. 4. P. 1283–1294.
16. Bureau T.E., Wessler S.R. Stowaway: a new family of invertedrepeat elements associated with genes of both monocotyledonous and dicotyledonous plants // Plant Cell. 1994. V. 6. P. 907–916.
17. Castilho A., Heslop-Harrison J.S. Physical mapping of 5S and 18S-25S rDNA and repetitive DNA sequences in Aegilops umbellulata // Genome. 1995. V. 38. P. 91–96.
18. Charlesworth B., Sniegowski P., Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes // Nature. 1994. V. 371. P. 215–220.
19. Copenhaver G.P., Pikaard C.S. RFLP and physical mapping with an rDNA-specifi c endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4 // Plant J. 1996. V. 9. P. 259–272.
20. Cox A.V., Bennett M.D., Dyer T.A. Specifi c 5S ribosomal RNA primers for plant species identifi cation in admixtures // Theor. Appl. Genet. 1992. V. 83. P. 684.
21. Cuadrado A., Jouve N. Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale // J. Hered. 2002. V. 93. P. 339–345.
22. Cullis C.A. Mechanisms and control of rapid genomic changes in fl ax // Ann. Bot. 2005. V. 95. P. 201–206.
23. Daboussi M., Capy P. Transposable elements in fi lamentous fungi // Annu. Rev. Microbiol. 2003. V. 57. P. 275–299.
24. Dvorák J., Luo M.C., Yang Z.L. Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and crossfertilizing Aegilops species // Genetics. 1998. V. 148. P. 423–434.
25. Feschotte C., Pritham E.J. DNA transposons and the evolution of eukaryotic genomes // Annu. Rev. Genet. 2007. V. 41. P. 331–368.
26. Flavell R.B. Amplifi cation, deletion and rearrangement: Major sources of variation during species divergence // Genome Evolution / Eds G.A. Dover, R.B. Flavell. London: Acad. Press, 1982.
27. Flavell R.B. Repetitive DNA and chromosome evolution in plants // Philos. T. R. Soc. Lon. B. 1986. V. 312. P. 227–242.
28. Flavell R.B., Bennett M.D., Smith J.B., Smith D.B. Genome size and the proportion of repeated nucleotide sequence DNA in plants // Biochem. Genet. 1974. V. 12. P. 257–269.
29. Flavell R.B., O’Dell M. Ribosomal RNA genes on homologous chromosomes of groups 5 and 6 in hexaploid wheat // Heredity. 1976. V. 37. P. 372–385.
30. Flavell A.J., Dunbar E., Anderson R. et al. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants // Nucl. Acids Res. 1992. V. 20. P. 3639–3644.
31. Frey M., Reinecke J., Grant S. et al. Excision of the En/Spm transposable element of Zea mays requires two elementencoded proteins // EMBO J. 1990. V. 9. P. 4037–4044.
32. Gerlach W.L., Bedbrook J.R. Cloning and characterization of ribosomal RNA genes from wheat and barley // Nucl. Acid Res. 1979. V. 7. P. 1869–1885.
33. Gerlach W.L., Dyer T.A. Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes // Nucl. Acids Res. 1980. V. 8. P. 4851–4865.
34. Heslop-Harrison J.S. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes // Plant Cell. 2000. V. 12. P. 617–636.
35. Hu T.T., Pattyn P., Bakker E.G., Cao J. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change // Nat. Genet. 2011. V. 43. P. 476–481.
36. Jurka J., Kapitonov V.V. PIFs meet Tourists and Harbingers: a superfamily reunion // Proc. Natl Acad. Sci. USA. 2001. V. 98. P. 12315–12316.
37. Kajikawa M., Okada N. LINEs mobilize SINEs in the eel through a shared 3′ sequence // Cell. 2002. V. 111. P. 433–444.
38. Kapitonov V., Jurka J. Rolling-circle transposons in eukaryotes // Proc. Natl Acad. Sci. USA. 2001. V. 98. P. 8714–8719.
39. Kilian A., Kleinhofs A. Cloning and mapping of telomere-associated sequences from Hordeum vulgare L. // Mol. Gen. Genet. 1992. V. 235. P. 153–156.
40. Kishii M., Tsujimoto H. Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat // Genome. 2002. V. 45. P. 946–955.
41. Kit S. Equilibrium sedimentation in density gradients of DNA preparations from animal tissues // J. Mol. Biol. 1961. V. 3. P. 711–716.
42. Kramerov D., Vassetzky N. Short retroposons in eukaryotic genomes // Int. Rev. Cytol. 2005. V. 247. P. 165–221.
43. Kubis S.E., Schmidt, T., Heslop-Harrison J.S. Repetitive DNA elements as a major component of plant genomes // Ann. Bot. 1998. V. 82. Р. P. 45–55.
44. Kumar A., Bennetzen J. Plant retrotransposons // Annu. Rev. Genet. 1999. V. 33. P. 479–532.
45. Laurie D.A., Bennett M.D. Nuclear DNA content in the genera Zea and Sorghum. Intergeneric, interspecifi c and intraspecific variation // Heredity. 1985. V. 55. P. 307–313.
46. Leitch I.J., Beaulieu J.M., Cheung K., Hanson L. et al. Punctuated genome size evolution in Liliaceae // J. Evol. Biol. 2007. V. 20. P. 2296–2308.
47. Linares C., Ferrer E., Fominaya A. Discrimination of the closely related A and D genomes of the hexaploid oat Avena sativa L. // Proc. Natl Acad. Sci. USA. 1998. V. 95. P. 12450–12455.
48. Lysak M.A., Koch M.A., Beaulieu J.M., Meister A., Leitch I.J. The dynamic ups and downs of genome size evolution in Brassicaceae // Mol. Biol. Evol. 2009. V. 26. P. 85–98.
49. Ma X.F., Gustafson J.P. Allopolyploidization-accommodated genomic sequence changes in Triticale // Ann. Bot. 2008. V. 101. P. 825–832.
50. McIntyre C.L., Pereira S., Moran L.B., Appels R. New Secale cereale (rye) DNA derivatives for the detection of rye chromosome segments in wheat // Genome. 1990. V. 33. P. 635–640.
51. Ming R., Hou S., Feng Y. et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya L.) // Nature. 2008. V. 452. P. 991–996.
52. Mitra R., Bhatia C.R. Repeated DNA sequences and polyploidy in cereal crops // DNA Systematics. V. II. Plants / Ed. S.K. Dutta. Boca Raton, Florida: CRC Press, 1986. P. 21–43.
53. Murata M., Heslop-Harrison J.S., Motoyoshi F. Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones // Plant J. 1997. V. 12. P. 31–37.
54. Nagaki K., Tsujimoto H., Isono K., Sasakuma T. Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae // Genome. 1995. V. 38. P. 479–486.
55. Nagaki K., Tsujimoto H., Sasakuma T.H. Genome specific repetitive sequence, pEt2, of Elimus trachycaulus
56. in part of Afa family of Triticeae // Genome. 1998. V. 41. P. 134–136.
57. Navratilova A., Koblizkova A., Macas J. Survey of extrachromosomal circular DNA derived from plant satellite repeats // BMC Plant Biol. 2008. V. 8. P. 90.
58. Ozkan H., Tuna M., Kilian B., Mori N., Ohta S. Genome size variation in diploid and tetraploid wild wheats // AoB Plants. 2010. doi: 10.1093/aobpla/plq015.
59. Paillard S., Schnurbusch T., Winzeler M., Messmer M. et al. An integrative genetic linkage map of winter wheat (Triticum aestivum L.) // Theor. Appl. Genet. 2003. V. 107. P. 1235–1242.
60. Paux E., Roger D., Badaeva E., Gay G. et al. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B // Plant J. 2006. V. 48. P. 463–474.
61. Pestsova E., Ganal M.W., Rцder M.S. Isolation and mapping of microsatellite markers specifi c for the D genome of bread wheat // Genome. 2000a. V. 43. P. 689–697.
62. Poulter R., Goodwin T. DIRS 1 and the other tyrosine recombinase retrotransposons // Cytogenet. Genome Res. 2005. V. 110. P. 575–588.
63. Rayburn A.L., Gill B.S. Isolation of a D-genome specific repeated DNA sequence from Aegilops squarosa // Plant Mol. Biol. 1986. V. 4. P. 102–109.
64. Reeder R.H. Enhancers and ribosomal gene spacers // Cell. 1984. V. 38. P. 349–351.
65. Rubin E., Lithwick G., Levy A.A. Structure and evolution of the hAT transposon superfamily // Genetics. 2001. V. 158. P. 949–957.
66. Sabot F., Schulman A.H. Parasitism and the retrotransposon life cycle in plants: a hitchhiker’s guide to the genome // Heredity. 2006. V. 97. P. 381–388.
67. Salina E.A., Adonina I.G., Vatolina T.Yu., Kurata N.A. Comparative analysis of the composition and organization of two subtelomeric repeat families in Aegilops speltoides Tausch. and related species // Genetica. 2004. V. 122. P. 227–237.
68. Salina E.A., Lim Y.K., Badaeva E.D. et al. Philogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat poliploids // Genome. 2006. V. 49. P. 1023–1035.
69. Salina E.A., Pestsova E.G., Adonina I.G., Vershinin A.V. Identification of a new family of tandem repeats in Triticeae genomes // Euphytica. 1998. V. 100. P. 231–237.
70. SanMiguel P., Gaut B.S., Tikhonov A., Nakajima Y., Bennetzen J.L. The paleontology of intergene retrotransposons in maize // Nature Genet. 1998. V. 20. P. 43–45.
71. SanMiguel P., Tikhonov A., Jin Y.K. et al. Nested retrotransposons in the intergenic regions of the maize genome // Science. 1996. V. 274. P. 765–768.
72. Schmidt T., Heslop-Harrison J.S. Genomes, genes and junk: the large-scale organization of plant chromosomes // Trends Plant Sci. 1998. V. 3. P. 195–199.
73. Schranz M.E., Mohammadin S., Edger P.P. Ancient whole genome duplications, novelty and diversifi cation: the WGD Radiation Lag-Time Model // Curr. Opin. Plant Biol. 2012. V. 15. P. 147–153.
74. Sharma S., Raina S.N. Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes // Cytogenet. Genome Res. 2005. V. 109. P. 15–26.
75. Somers D.J., Isaac P., Edwards K. et al. A high-density wheat microsatellite consensus map for bread wheat (Triticum aestivum L.) // Theor. Appl. Genet. 2004. V. 109. P. 1105–1114.
76. Suoniemi A., Tanskanen J., Schulman A.H. Gypsy-like retrotransposons are widespread in the plant kingdom // Plant J. 1998. V. 13. P. 699–705.
77. Sýkorová E., Lim K.Y., Kunická Z., Chase M.W. et al. Telo mere variability in the monocotyledonous plant
78. order Asparagales // Proc. Biol. Sci. 2003. V. 270. P. 1893–1904.
79. Vershinin A.V., Schwarzacher T., Heslop-Harrison J.S. The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes // Plant Cell. 1995. V. 7. P. 1823–1833.
80. Vicient C.M., Kalendar R., Anamthawat-Jonsson K., Schulman A.H. Structure, functionality, and evolution of the BARE 1 retrotransposon of barley // Genetica. 1999. V. 107. P. 53–63.
81. Vicient C.M., Kalendar R., Schulman A.H. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants // Genome Res. 2001. V. 11. P. 2041–2049.
82. Vincentz M., Flavell R. Mapping of ribosomal RNA transcripts in wheat // Plant Cell. 1989. V. 1. P. 579–589.
83. Vitte C., Bennetzen J.L. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution // Proc. Natl Acad. Sci. USA. 2006. V. 103. P. 17638–17643.
84. Vitte C., Panaud O. LTR retrotransposons and fl owering plant genome size: emergence of the increase/decrease model // Cytogenet. Genome Res. 2005. V. 110. P. 91–107.
85. Voytas D.F., Cummings M.P., Konieczny A.K. et al. Copia-like retrotransposons are ubiquitous among plant // Proc. Natl Acad. Sci. USA. 1992. V. 89. P. 7124–7128.
86. Wicker T., Guyot R., Yahiaoui N., Keller B. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements // Plant Physiol. 2003. V. 132. P. 52–63.
87. Wicker T., Sabot F., Hua-Van A., Bennetzen J.L. et al. A unified classification system for eukaryotic transposable elements // Nat. Rev. Genet. 2007. V. 8. P. 973–982.
88. Xu L., Chen H., Hu X., Zhang R. et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms // Mol. Biol. Evol. 2006. V. 23. P. 1107–1108.
89. Zhang P., Friebe B., Gill B.S. Variation in the distribution of a genome-specifi c DNA sequences on chromosomes reveals evolutionary relations in the Triticum and Aegilops complex // Plant Syst. Evol. 2002. V. 235. P. 169–179.
90. Zupunski V., Gubensek F., Kordis D. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons // Mol. Biol. Evol. 2001. V. 18. P. 1849–1863.
Рецензия
Просмотров:
1080
Послать статью по эл. почте 