Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives

Annals of Botany

Volumn 104, Issue 5, 2009, Pages 873-881

  Wolny, Elzbieta ^a   Hasterok, Robert ^a  

^a UNIVERSITY OF SILESIA   (Poland)

Author keywords

25S rDNA; 5S rDNA; B. distachyon; Brachypodium; FISH; Flow cytometry; GISH; Nuclear genome size; Ribosomal RNA genes

Indexed keywords

PLANT DNA; RIBOSOME RNA;

CHROMOSOME; COMPARATIVE STUDY; CYTOLOGY; ENZYME ACTIVITY; FLOW CYTOMETRY; FLUORESCENCE; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; GENOTYPE; GRASS; SUBSPECIES;

ARTICLE; COMPARATIVE STUDY; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; PHYLOGENY; PLANT CHROMOSOME; PLANT GENOME; POACEAE;

CHROMOSOMES, PLANT; DNA, PLANT; FLOW CYTOMETRY; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; PHYLOGENY; POACEAE; RNA, RIBOSOMAL;

BRACHYPODIUM; BRACHYPODIUM DISTACHYON; BRACHYPODIUM PHOENICOIDES; BRACHYPODIUM PINNATUM; BRACHYPODIUM RETUSUM; POACEAE;

EID: 70349587942     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcp179     Document Type: Article

References (49)

1. Adams SP, Leitch IJ, Bennett MD, Chase MW, Leitch AR. 2000. Ribosomal DNA evolution and phylogeny in Aloe (Asphodelaceae). American Journal of Botany 87: 1578-1583.
2. Ali HB, Lysak MA, Schubert I. 2004. Genomic in situ hybridization in plants with small genomes is feasible and elucidates the chromosomal parentage in interspecific Arabidopsis hybrids. Genome 47: 954-960.
3. Belyayev A, Raskina O, Nevo E. 2001. Evolutionary dynamics and chromosomal distribution of repetitive sequences on chromosomes of Aegilops speltoides revealed by genomic in situ hybridization. Heredity 86: 738-742.
4. Benabdelmouna A, Abirached-Darmency M, Darmency H. 2001. Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S and 18S-5 8S-25S rDNA genes. Theoretical and Applied Genetics 103: 668-677.
5. Bennett MD, Leitch IJ. 2004. Plant DNA C-values database (release 3.0, December 2004) http://www.kew.org/cvalues/homepage.html
6. Catalan P, Olmstead RG. 2000. Phylogenetic reconstruction of the genus Brachypodium Beauv. (Poaceae) from combined sequences of chloroplast gene and nuclear ITS. Plant Systematics and Evolution 220: 1-19.
7. Catalan P, Shi Y, Armstrong L, Draper J, Stace CA. 1995. Molecular phy-logeny of the grass genus Brachypodium P-Beauv based on RFLP and RAPD analysis. Botanical Journal of the Linnean Society 117: 263-280.
8. Catalan P, Kellogg EA, Olmstead RG. 1997. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Molecular Phylogenetics and Evolution 8: 150-166.
9. Dolezel J, Bartos J. 2005. Plant DNA flow cytometry and estimation of nuclear genome size. Annals of Botany 95: 99-110.
10. Dolezel J, Sgorbati S, Lucretti S. 1992. Comparison of three DNA fluoro-chromes for flow cytometric estimation of nuclear DNA content in plants. Physiologia Plantarum 85: 625-631.
11. Draper J, Mur LAJ, Jenkins G, et al. 2001. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology 127: 1539-1555.
12. Dubcovsky J, Dvorak J. 1995. Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics 140: 1367-1377.
13. Falistocco E, Torricelli R, Falcinelli M. 2002. Genomic relationships between Medicago murex Willd. and Medicago lesinsii E. Small. investigated by in situ hybridization. Theoretical and Applied Genetics 105: 829-833.
14. Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G. 1998. Cytogenetics for the model system Arabidopsis thaliana. The Plant Journal 13: 867-876.
15. Garvin DF, Gu YQ, Hasterok R, et al. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research Crop Science - The Plant Genome 48 S69-S84
16. Gerlach WL, Dyer TA. 1980. Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucleic Acids Research 8: 4851-4865.
17. Greilhuber J. 2005. Intraspecific variation in genome size in angiosperms: identifying its existence. Annals of Botany 95: 91-98.
18. Greilhuber J. 2008. Cytochemistry and C-values: the less-well-known world of nuclear DNA amounts. Annals of Botany 101: 791-804.
19. Hajdera I, Siwinska D, Hasterok R, Maluszynska J. 2003. Molecular cyto-genetic analysis of genome structure in Lupinus angustifolius and Lupinus cosentinii. Theoretical and Applied Genetics 107: 988-996.
20. Hasterok R, Jenkins G, Langdon T, Jones RN, Maluszynska J. 2001. Ribosomal DNA is an effective marker of Brassica chromosomes. Theoretical and Applied Genetics 103: 486-490.
21. Hasterok R, Draper J, Jenkins G. 2004. Laying the cytotaxonomic foundations of a new model grass, Brachypodium distachyon (L.) Beauv. Chromosome Research 12: 397-403.
22. Hasterok R, Dulawa J, Jenkins G, Leggett M, Langdon T. 2006a. Multi-substrate chromosome preparations for high throughput comparative FISH. BMC Biotechnology 6: 20. doi:10.1186/1472-6750-6-20 (Pubitemid 43933060)
23. Hasterok R, Wolny E, Hosiawa M, et al. 2006b. Comparative analysis of rDNA distribution in chromosomes of various species of Brassicaceae. Annals of Botany 97: 205-216.
24. Hasterok R, Marasek A, Donnison IS, et al. 2006c. Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173: 349-362.
25. Hsiao C, Chatterton NJ, Asay KH, Jensen KB. 1995. Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences. Genome 38: 211-223.
26. Huo N, Gu YQ, Lazo GR, et al. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49: 1099-1108.
27. Huo N, Vogel JP, Lazo GR, et al. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology 70: 47-61.
28. Jenkins G, Hasterok R. 2007. BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment. Nature Protocols 2: 88-98.
29. Kim NS, Fedak G, Han F, Cao W. 2008. Cytogenetic analyses of intergeneric hybrids between barley and nine species of Elymus. Genome 51: 897-904.
30. Kopecky D, Lukaszewski AJ, Dolezel J. 2008. Meiotic behaviour of individual chromosomes of Festuca pratensis in tetraploid Lolium multiflorum. Chromosome Research 16: 987-998.
31. Li C-B, Zhang D-M, Ge S, Lu B-R, Hong D-Y. 2001a. Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza offi-cinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theoretical and Applied Genetics 103: 197-203.
32. Li C-B, Zhang D-M, Ge S, Lu B-R, Hong D-Y. 2001b. Identification of genome constitution of Oryza malampuzhaensis, O. minuta, and O. punctata by multicolor genomic in situ hybridization. Theoretical and Applied Genetics 103: 204-211.
33. Lim KY, Kovarik A, Matyasek R, Bezdek M, Lichtenstein CP, Leitch AR. 2000. Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109: 161-172.
34. Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. 2006. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proceedings of the National Academy of Sciences of the USA 103: 5224-5229.
35. Maluszynska J. 2002. In situ hybridization in plants - methods and application. In: Jain SM. ed. Molecular techniques in crop improvement. Kluwer Academic Publishers, 299-326.
36. Maluszynska J, Hasterok R. 2005. Identification of individual chromosomes and parental genomes in Brassica juncea using GISH and FISH. Cytogenetic and Genome Research 109: 310-314.
37. Mandakova T, Lysak MA. 2008. Chromosomal phylogeny and karyotype evolution in x 7 crucifer species (Brassicaceae). The Plant Cell 20: 2559-2570.
38. Marasek A, Hasterok R, Wiejacha K, Orlikowska T. 2004. Determination by GISH and FISH of hybrid status in Lilium. Hereditas 140: 1-7.
39. Molnar I, Benavente E, Molnar-Lang M. 2009. Detection of intergenomic chromosome rearrangements in irradiated Triticum aestivum - Aegilops biuncialis amphiploids by multicolour genomic in situ hybridization. Genome 52: 156-165.
40. Murray MG, Thompson WF. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 4321-4325.
41. Naganowska B, Zielinska A. 2002. Physical mapping of 18S-25S rDNA and 5S rDNA in Lupinus via fluorescent in situ hybridization. Cellular & Molecular Biology Letters 7: 665-670.
42. Naganowska B, Zielinska A. 2004. Localisation of rDNA in the Lupinus genome during the cell cycle. Journal of Applied Genetics 45: 189-193.
43. Pendinen G, Gavrilenko T, Jiang J, Spooner DM. 2008. Allopolyploid spe-ciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization. Genome 51: 714-720.
44. Robertson IH. 1981. Chromosome numbers in Brachypodium Beauv. (Gramineae). Genetica 56: 55-60.
45. Sharma ML. 1979. Some considerations on the phylogeny and chromosomal evolution in grasses. Cytologia 44: 679-685
46. Shi Y, Draper J, Stace CA. 1993. Ribosomal DNA variation and its phyloge-netic implication in the genus Brachypodium (Poaceae). Plant Systematics and Evolution 188: 125-138.
47. Singh RJ, Kim HH, Hymowitz T. 2001. Distribution of rDNA loci in the genus Glycine Willd. Theoretical and Applied Genetics 103: 212-218.
48. Smarda P, Bures P, Horova L, Rotreklova O. 2008. Intrapopulation genome size dynamics in Festuca pallens. Annals of Botany 102: 599-607.
49. Weiss-Schneeweiss H, Stuessy TF, Siljak-Yakovlev S, Baeza CM, Parker J. 2003. Karyotype evolution in South American species of Hypochaeris (Asteraceae, Lactuceae). Plant Systematics and Evolution 241: 171-184.