Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes

Genetics

Volumn 162, Issue 3, 2002, Pages 1389-1400

  Ramakrishna, Wusirika ^a   Dubcovsky, Jorge ^b   Park, Yong Jin ^a,d   Busso, Carlos ^b   Emberton, John ^a   SanMiguel, Phillip ^c   Bennetzen, Jeffrey L ^a  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c PURDUE UNIVERSITY   (United States)

^d National Institute of Animal Science   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR RNA; PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BARLEY; CEREAL; CHROMOSOME INVERSION; DNA SEQUENCE; GENE DUPLICATION; GENE REARRANGEMENT; GENE STRUCTURE; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; ORTHOLOGY; PLANT GENETICS; PRIORITY JOURNAL; RETROPOSON; RICE; RNA GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SORGHUM; TRANSPOSON; WHEAT; EVOLUTION; GENETICS; MOLECULAR GENETICS; POINT MUTATION;

CEREALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA TRANSPOSABLE ELEMENTS; EVOLUTION; GENOME, PLANT; MOLECULAR SEQUENCE DATA; POINT MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 0036861524     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (73)

1. Arumuganathan, K., and E. D. Earle, 1991 Nuclear DNA content of some important plant species. Plant Mol. Biol. Reporter 9: 208-218.
2. Barakat, A., N. Carels and G. Bernardi, 1997 The distribution of genes in the genomes of Gramineae. Proc. Natl. Acad. Sci. USA 94: 6857-6861.
3. Bennett, M. D., and J. B. Smith, 1976 Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 274: 227- 274.
4. Bennett, M. D., P. Bhandol and I. J. Leitch, 2000 Nuclear DNA amounts in angiosperms and their modern uses: 807 New estimates. Ann. Bot. 86: 859-909.
5. Bennetzen, J. L., 2000 Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1030.
6. Bennetzen, L., and M. Freeling, 1993 Grasses as a single genetic system: Genome composition, collinearity and compatibility. Trends Genet. 9: 259-261.
7. Bennetzen, J. L., and W. Ramakrishna, 2002 Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol. Biol. 48: 821-827.
8. Blanc, G., A. Barakat, R. Guyot, R. Cooke and M. Delseny, 2000 Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101.
9. Brown, J. W. S., G. P. Clark, D. J. Leader, C. G. Simpson and T. Lowe, 2001 Multiple snoRNA gene clusters from Arabidopsis. RNA 7: 1817-1832.
10. Bureau, T. E., and S. R. Wessler, 1994 Mobile inverted-repeat elements of the tourist family are associated with the genes of many cereal grasses. Proc. Natl. Acad. Sci. USA 91: 1411-1415.
11. Chen, M., P. Sanmiguel, A. C. D. Oliveira, S.-S. Woo, H. Zhang et al., 1997 Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. USA 94: 3431-3435.
12. Chen, M., P. Sanmiguel and J. L. Bennetzen, 1998 Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435-443.
13. Devos, K. M., J. K. M. Brown and J. L. Bennetzen, 2002 Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.
14. Dubcovsky, J., and J. Dvorak, 1995 Ribosomal Rna multigene loci: Nomads of the Triticeae genomes. Genetics 140: 1367-1377.
15. Dubcovsky, J., D. Lijavetzky, L. Appendino and G. Tranquilli, 1998 Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement. Theor. Appl. Genet. 97: 968-975.
16. Dubcovsky, J., W. Ramakrishna, P. Sanmiguel, C. S. Busso, L. Yan et al., 2001 Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol. 125: 1342-1353.
17. Faris, J. D., K. M. Haen and B. S. Gill, 2000 Saturation mapping of a gene-rich recombinant hot spot region in wheat. Genetics 154: 823-835.
18. Feuillet, C., and B. Keller, 1999 High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. USA 96: 8265-8270.
19. Feuillet, C., A. Penger, K. Gellner, A. Mast and A. Keller, 2001 Molecular evolution of receptor-like kinase genes in hexaploid wheat: Independent evolution of orthologs after polyploidization and mechanisms of local rearrangements at paralogous loci. Plant Physiol. 125: 1304-1313.
20. Freeling, M., 2001 Grasses as a single genetic system: Reassessment. Plant Physiol. 125: 1191-1197.
21. Gale, M. D., and K. M. Devos, 1998 Comparative genetics in the grasses. Proc. Natl. Acad. Sci. USA 95: 1971-1974.
22. Gaut, B. S., 1998 Molecular clocks and nucleotide substitution rates in higher plants. Evol. Biol. 30: 93-120.
23. Gaut, B. S., B. R. Morton, B. C. McCaig and M. T. Clegg, 1996 Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcl. Proc. Natl. Acad. Sci. USA 93: 10274-10279.
24. Gaut, B. S., A. S. Peek, B. R. Morton and M. T. Clegg, 1999 Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae). Mol. Biol. Evol. 16: 1087-1097.
25. Gill, K. S., B. S. Gill, T. R. Endo and E. V. Boyko, 1996a Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143: 1001-1012.
26. Gill, K. S., B. S. Gill, T. R. Endo and T. Taylor, 1996b Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144: 1883-1891.
27. Hulbert, S. H., C. A. Webb, S. M. Smith and Q. Sun, 2001 Resistance gene complexes: Evolution and utilization. Annu. Rev. Phytopathol. 39: 285-312.
28. Jukes, T. H., and C. R. Cantor, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism, edited by H. N. MUNRO. Academic Press, New York.
29. Kato, K., H. Miura and S. Sawada, 1999 Comparative mapping of the wheat Vrn1 region with the rice Hd-6 region. Genome 42: 204-209.
30. Keller, B., and C. Feuillet, 2000 Colinearity and gene density in grass genomes. Trends Plant Sci. 5: 246-251.
31. Klein, P. E., R. R. Klein, S. W. Cartinhour, P. E. Ulanch, J. M. Dong et al., 2000 A high-throughput AFLP-based method for constructing integrated genetic and physical maps: Progress toward a sorghum genome map. Genome Res. 10: 789-807.
32. Kleinhofs, A., A. Kilian, M. A. Saghai, R. M. Biyashev, P. Hayes et al., 1993 A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor. Appl. Genet. 86: 705-712.
33. Ku, H.-M., T. Vision, J. Liu and S. D. Tanksley, 2000 Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97: 9121-9126.
34. Kumar, S., K. Tamura, I. B. Jakobsen and M. Nei, 2001 MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
35. Kunzel, G., L. Korzun and A. Meister, 2000 Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154: 397-412.
36. Lagercrantz, U., 1998 Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150: 1217-1228.
37. Leader, D. J., G. P. Clark, J. Watters, A. F. Beven, P. J. Shaw et al., 1997 Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs. EMBO J. 16: 5742-5751.
38. Leader, D. J., G. P. Clark, J. Watters, A. F. Beven, P. J. Shaw et al., 1999 Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs. Plant Mol. Biol. 39: 1091-1100.
39. Leister, D., J. Kurth, D. A. Laurie, M. Yano, T. Sasaki et al., 1998 Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl. Acad. Sci. USA 95: 370-375.
40. Lijavetzky, D., G. Muzzi, T. Wicker, B. Keller, R. Wing et al., 1999 Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42: 1176-1182.
41. Lynch, M., and J. S. Conery, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
42. Lynch, M., and J. C. Conery, 2001 Gene duplication and evolution: Response. Science 293: U2-U3.
43. Meyers, B. C., S. V. Tingley and M. Morgante, 2001 Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11: 1660-1676.
44. Moore, G., K. M. Devos, Z. Wang and M. D. Gale, 1995 Grasses, line up and form a circle. Curr. Biol. 5: 737-739.
45. Nei, M., and T. Gojobori, 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
46. O'Neill, C., and I. Bancroft, 2000 Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23: 233-243.
47. Panstruga, R., R. Buschges, P. Piffanelli and P. Schulze-Lefert, 1998 A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in monocot genome. Nucleic Acids Res. 26: 1056-1062.
48. Richly, E., J. Kurth and D. Leister, 2002 Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol. Biol. Evol. 19: 76-84.
49. Rossberg, M., K. Theres, A. Acarkan, R. Herrero, T. Schmitt et al., 2001 Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13: 979-988.
50. Sanmiguel, P., and J. L. Bennetzen, 1998 Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82: 37-44.
51. Sanmiguel, P., A. Tikhonov, Y.-K. Jin, N. Motchoulskaia, D. Zakharov et al., 1996 Nested retrotransposon in the intergenic regions of the maize genome. Science 274: 765-768.
52. Sanmiguel, P., B. S. Gaut, A. Tikhonov, Y. Nakajima and J. L. Bennetzen, 1998 The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43-45.
53. m. Funct. Integr. Genomics 2: 70-80.
54. Sarma, R. N., B. S. Gill, T. Sasaki, G. Galiba, J. Sutka et al., 1998 Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time. Theor. Appl. Genet. 97: 103-109.
55. Shirasu, K., A. H. Schulman, T. Lahaye and P. Schulze-Lefert, 2000 A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908-915.
56. Stebbins, G. L., 1981 Coevolution of grasses and herbivores. Ann. Mo. Bot. Gard. 68: 75-86.
57. Stein, N., C. Feuillet, T. Wicker, E. Schlagenhauf and B. Keller, 2000 Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc. Natl. Acad. Sci. USA 97: 13436-13441.
58. Sutka, J., G. Galiba, A. Vagujfalvi, B. S. Gill and J. W. Snape, 1999 Physical mapping of the Vrn-A1 and Fr1 genes on chromosome 5A of wheat using deletion lines. Theor. Appl. Genet 99: 199-202.
59. Tajima, F., 1993 Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135: 599-607.
60. Tarchini, R., P. Biddle, R. Wineland, S. Tingey and A. Rafalski, 2000 The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381-391.
61. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin and D. G. Higgins, 1997 The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
62. Tikhonov, A. P., P. J. Sanmiguel, Y. Nakajima, N. M. Gorenstein, J. L. Bennetzen et al., 1999 Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA 96: 7409-7414.
63. Van de Peer, Y., J. S. Taylor, I, Braasch and A. Meyer, 2001 The ghost of selection past: Rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53: 436-446.
64. Vision, T. J., D. G. Brown and S. D. Tanksley, 2000 The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
65. Wagner, A., 2001 Birth and death of duplicated genes in completely sequenced eukaryotes. Trends Genet. 17: 237-239.
66. Wicker, T., N. Stein, L. Albar, C. Feuillet, E. Schlagenhauf et al., 2001 Analysis of a contigous 211 kb sequence in diploid wheat (Triticum monococcum L) reveals multiple mechanisms of genome evolution. Plant J. 26: 307-316.
67. Wolfe, K. H., and P. M. Sharp, 1993 Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37: 441-456.
68. Wolfe, K. H., and D. Shields, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708- 713.
69. Wolfe, K. H., W.-H. Li and P. M. Sharp, 1987 Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84: 9054-9058.
70. Wolfe, K. H., M. Gouy, Y.-W. Yang, P. M. Sharp and W.-H. Li, 1989a Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86: 6201-6205.
71. Wolfe, K. H., P. M. Sharp and W.-H. Li, 1989b Rates of synonymous substitution in plant nuclear genes. J. Mol. Evol. 29: 208-211.
72. Yu, Y., J. P. Tomkins, R. Waugh, D. A. Frisch, D. Kudrna et al., 2000 A bacterial artificial chromosome library for barley (Hordeum vulgare). Theor. Appl. Genet 101: 1093-1099.
73. Zhang, L. Q., S. K. Pond and B. S. Gaut, 2001 A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J. Mol. Evol. 52: 144-156.