Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions

Plant Cell

Volumn 12, Issue 7, 2000, Pages 1021-1029

  Bennetzen, Jeffrey L ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROCOLINEARITY; PLANT GENOME; SEQUENCE ANALYSIS;

EMBRYOPHYTA;

EID: 0033869323     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.12.7.1021     Document Type: Article

References (78)

1. Ahn, S., Anderson, J.A., Sorrells, M.E., and Tanksley, S.D. (1993). Homoeologous relationships of rice, wheat and maize chromosomes. Mol. Gen. Genet. 241, 483-490.
2. Ananiev, E.V., Phillips, R.L., and Rines, H.W. (1998). Complex structure of knob DNA on maize chromosome 9: Retrotransposon invasion into heterochromatin. Genetics 149, 2025-2037.
3. Arumuganathan, K., and Earle, E.D. (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218.
4. Avramova, Z., Tikhonov, A., SanMiguel, P., Jin, Y.-K., Liu, C., Woo, S.-S., Wing, R.A., and Bennetzen, J.L. (1996). Gene identification in a complex chromosomal continuum by local genomic cross-referencing. Plant J. 10, 1163-1168.
5. Bennett, M.D., and Leitch, I.J. (1995). Nuclear DNA amounts in angiosperms. Ann. Bot. 76, 113-176.
6. Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42, 251-269.
7. Bennetzen, J.L., and Freeling, M. (1993). Grasses as a single genetic system: Genome composition, collinearity and compatibility. Trends Genet. 9, 259-261.
8. Bennetzen, J.L., and Freeling, M. (1997). The unified grass genome: Synergy in synteny. Genome Res. 7, 301-307.
9. Bennetzen, J.L., and Kellogg, E.A. (1997). Do plants have a one-way ticket to genomic obesity? Plant Cell 9, 1509-1514.
10. Bennetzen, J.L, SanMiguel, P., Chen, M., Tikhonov, A., Francki, M., and Arromova, Z. (1998) Grass genomes. Proc. Natl. Acad. Sci. USA 95, 1975-1978.
11. Bennetzen, J.L., Schrick, K., Springer, P.S., Brown, W.E., and SanMiguel, P. (1994). Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565-576.
12. Blanc, G., Barakat, A., Guyot, R., Cooke, R., and Delseny, M. (2000). Extensive duplication and reshuffling in the Arabidopsis thaliana genome. Plant Cell 12, 1093-1101.
13. Bonierbale, M.D., Plaisted, R.L., and Tanksley, S.D. (1988). RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120, 1095-1103.
14. Chao, S., Sharp, P.J., Worland, A.J., Warham, E.J., Koebner, R.M.D., and Gale, M.D. (1989). RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78, 495-504.
15. Chen, M. (1998). The Structure of sh2/a1-Homologous Regions in Maize, Rice and Sorghum. Ph.D. Dissertation (West Lafayette, IN: Purdue University).
16. Chen, M., and Bennetzen, J.L. (1996). Sequence composition and organization in the Sh2/A1-homologous region of rice. Plant Mol. Biol. 32, 999-1001.
17. Chen, M., SanMiguel, P., and Bennetzen, J.L. (1998). Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148, 435-443.
18. Copenhaver, G.P., et al. (1999). Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286, 2468-2474.
19. Crepet, W.L., and Feldman, G.D. (1991). The earliest remains of grasses in the fossil record. J. Bot. 78, 1010-1014.
20. Cresse, A.D., Hulbert, S.H., Brown, W.E., Lucas, J.R., and Bennetzen, J.L. (1995). Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140, 315-324.
21. Devos, K.M., Atkinson, M.D., Chinoy, C.N., Harcourt, R.L., Koebner, R.M.D., Liu, C.J., Masojc, P., Xie, D.X., and Gale, M.D. (1993). Chromosomal rearrangements in the rye genome relative to that of wheat. Theor. Appl. Genet. 85, 673-680.
22. Devos, K.M., Dubcovsky, J., Dvorak, J., Chinoy, C.N., and Gale, M.D. (1995). Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination. Theor. Appl. Genet. 91, 282-288.
23. Devos, K.M., Beales, J., Nagamura, Y., and Sasaki, T. (1999). Arabidopsis-Rice: Will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res. 9, 825-829.
24. Devos, K.M., Pittaway, T.S., Reynolds, A., and Gale, M.D. (2000). Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor. Appl. Genet. 100, 190-198.
25. Doolittle, W.F., and Sapienza, C. (1980). Selfish genes, the pheno-type paradigm and genome evolution. Nature 284, 601-603.
26. Doyle, J.F., and Gaut, B.F. (2000). Plant Molecular Evolution. (Dordrecht, The Netherlands: Kluwer Academic Publishers).
27. Dunford, R.P., Kurata, N., Laurie, D.A., Money, T.A., Minobe, Y., and Moore, G. (1995). Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res. 23, 2724-2728.
28. Fatokun, C.A., Menacio, D.I., Danesh, D., and Young, N.D. (1992). Evidence for orthologous seed weight genes in cowpea and mungbean, based upon RFLP mapping. Genetics 132, 841-846.
29. Feuillet, C., and Keller, B. (1999). High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. USA 96, 8265-8270.
30. Flavell, R.B., Bennett, M.D., Smith, J.B., and Smith, D.B. (1974). Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12, 257-269.
31. Fransz, P.F., Armstrong, S., de Jong, J.H., Parnell, L.D., van Drunen, C., Dean, C., Zabel, P., Bisseling, T., and Jones, G.H. (2000). Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromere region. Cell 100, 367-376.
32. Gale, M.D., and Devos, K.M. (1998). Plant comparative genetics after 10 years. Science 282, 656-659.
33. Gaut, B.S., and Doebley, J.F. (1997). DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 88, 2060-2064.
34. Grant, D., Cregan, P., and Shoemaker, R.C. (2000). Genome organization in dicots. I. Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Acad. Sci. USA, 97, 4168-4173.
35. Han, F., Kilian, A., Chen, J.P., Kudrna, D., Steffenson, B., Yamamoto, K., Matsumoto, T., Sasaki, T., and Kleinhofs, A. (1999). Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42, 1071-1076.
36. Helentjaris, T., Weber, D.L., and Wright, S. (1988). Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118, 353-363.
37. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H., and Kanda, M. (1996). Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. USA 93, 7783-7788.
38. Holmquist, G.P., Kapitonov, V.V., and Jurka, J. (1998). Mobile genetic elements, chiasmata, and the unique organization of beta-heterochromatin. Cytogenet. Cell Genet. 80, 113-116
39. Hulbert, S.H., Richter, T.E., Axtell, J.D., and Bennetzen, J.L. (1990). Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc. Natl. Acad. Sci. USA 87, 4251-4255.
40. 2. Nature 376, 559-560.
41. Jiang, J., Nasuda, S., Dong, F., Scherrer, C.W., Woo, S.-S., Wing, R.A., Gill, B.S., and Ward, D.C. (1996). A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc. Natl. Acad. Sci. USA 93, 14210-14213.
42. Kaneko, T., Katoh, T., Sato, S., Nakamura, Y., Asamizu, E., Kotani, H., Miyajima, N., and Tabata, S. (1999). Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAG clones. DNA Res. 6, 183-195.
43. Kilian, A., Chen, J., Han, F., Steffenson, B., and Kleinhofs, A. (1997). Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol. Biol. 35, 187-195.
44. Kishimoto, N., Higo, H., Abe, K., Arai, S., Saito, A., and Higo, K. (1994). Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor. Appl. Genet. 88, 722-726.
45. 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.
46. Lagercrantz, U., Putterill, J., Coupland, G., and Lydiate, D. (1996). Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J. 9, 13-20.
47. Leister, D.M., Kurth, J., Laurie, D.A., Yano, M., Sasaki, T., Devos, K.M., Graner, A., and Schulze-Lefert, P. (1998). Rapid reorganisation of resistance gene homologues in cereal genomes. Proc. Natl. Acad. Sci. USA 95, 370-375.
48. Leutweiler, L.S., Hough-Evans, B.R., and Meyerowitz, E.M. (1984). The DNA of Arabidopsis thaliana. Mol. Gen. Genet. 194, 15-23.
49. Lin, X.Y., et al. (1999). Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768.
50. Llaca, V., and Messing, J. (1998). Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions. Plant J. 15, 211-220.
51. McClintock, B. (1984). The significance of responses of the genome to challenge. Science 226, 792-801.
52. McCombie, W.R., et al. (2000). The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100, 377-386.
53. Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D., and Koorneef, M. (1998). Arabidopsis thaliana: A model plant for genome analysis. Science 282, 679-682.
54. Michelmore, R.W., and Meyers, B.C. (1998). Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8, 1113-1130.
55. Moore, G., Devos, K.M., Wang, Z., and Gale, M.D. (1995). Grasses, line up and form a circle. Curr. Biol. 5, 737-739.
56. Nagamura, Y., Inoue, T., Antonio, B.A., Shimano, T., Kajiya, H., Shomura, A., Lin, S.Y., Kuboki, Y., Harushima, Y., Kurata, N., Minobe, Y., Yano, M., and Sasaki, T. (1995). Conservation of duplicated segments between rice chromosomes 11 and 12. Breed. Sci. 45, 373-376.
57. Orgel, L.E., and Crick, F.H.C. (1980). Selfish DNA: The ultimate parasite. Nature 284, 604-607.
58. Panstruga, R., Buschges, R., and Schulze-Lefert, P. (1998). A contiguous 60 kb genomic stretch from barley provides molecular evidence for gene islands in monocot genomes. Nucleic Acids Res. 26, 1056-1062.
59. Paterson, A.H., Lin, Y.-R., Li, Z., Schertz, K.F., Doebley, J.F., Pinson, S.R.M., Liu, S.-C., Stansel, J.W., and Irvine, J.E. (1995). Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269, 1714-1718.
60. Paterson, A.H., et al. (1996). Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genet. 14, 380-382.
61. Pebusque, M.-J., Coulier, F., Birnbaum, D., and Pontarotti, P. (1998). Ancient large-scale genome duplications: Phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145-1159.
62. Pelissier, T., Tutois, S., Tourmente, S., Deragon, J.M., and Pickard, G. (1996). DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97, 141-151.
63. Petrov, D.A., Lozovskaya, E.R., and Hartl, D.L. (1996). High intrinsic rate of DNA loss in Drosophila. Nature 384, 346-349.
64. Richter, T.E., and Ronald, P.C. (2000). The evolution of disease resistance genes. Plant Mol. Biol. 42, 195-204.
65. SanMiguel, P., and Bennetzen, J.L. (1998). Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82, 37-44.
66. SanMiguel, P., Tikhonov, A., Jin, Y.-K., Motchoulskaia, N., Zakharov, D., Melake Berhan, A., Springer, P.S., Edwards, K.J., Avramova, Z., and Bennetzen, J.L. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768.
67. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and Bennetzen, J.L. (1998). The paleontology of intergene retrotransposons of maize. Nature Genet. 20, 43-45.
68. Sanz-Alferez, S., Richter, T.E., Hulbert, S.H., and Bennetzen, J.L. (1995). The Rp3 disease resistance gene of maize: Mapping and characterization of introgressed alleles. Theor. Appl. Genet. 91, 25-32.
69. Sparrow, A.M., and Miksche, J.P. (1961). Correlations of nuclear volume and DNA content with higher plant tolerance to chronic radiation. Science 134, 182-183.
70. Springer, P.S. (1992). Genomic Organization of Zea mays and Its Close Relatives. Ph.D. Dissertation (West Lafayette, IN: Purdue University).
71. Sudupak, M.A., Bennetzen, J.L., and Hulbert, S.H. (1993). Unequal exchange and meiotic instability of the Rp1 region disease resistance genes in maize. Genetics 133, 119-125.
72. Tarchini, R., Biddle, P., Wineland, R., Tingey, S., and Rafalski, A. (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.
73. Tikhonov, A.P., SanMiguel, P.J., Nakajima, Y., Gorenstein, N.M., Bennetzen, J.L., and Avramova, Z. (1999). Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA 96, 7409-7414.
74. van Dodeweerd, A.M., Hall, C.R., Bent, E.G., Johnson, S.J., Bevan, M.W., and Bancroft, I. (1999). Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana. Genome 42, 887-892.
75. Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
76. Wessler, S.R., Bureau, T.E., and White, S.E. (1995). LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814-821.
77. Wolfe, K.H., and Shields, D.C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
78. Zhang, H., Jia, J., Gale, M.D., and Devos, K.M. (1998). Relationship between the chromosomes of Aegilops umbellulata and wheat. Theor. Appl. Genet. 96, 69-75.