How to usefully compare homologous plant genes and chromosomes as DNA sequences

Plant Journal

Volumn 53, Issue 4, 2008, Pages 661-673

  Lyons, Eric ^a   Freeling, Michael ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

CNS; Fractionation; Plant comparative genomics; Synteny

Indexed keywords

ALGORITHMS; CHROMOSOMES; GENE EXPRESSION; PLANTS (BOTANY); VISUALIZATION;

ALIGNMENT ALGORITHMS; HOMOLOGOUS PLANT GENES; NON-CODING SEQUENCES; PLANT COMPARATIVE GENOMICS;

DNA SEQUENCES;

ALGORITHM; ARABIDOPSIS; ARTICLE; BIOLOGY; GENE; GENETICS; GENOME; GENOMICS; MAIZE; METHODOLOGY; PLANT CHROMOSOME; RICE; SYNTENY;

ALGORITHMS; ARABIDOPSIS; CHROMOSOMES, PLANT; COMPUTATIONAL BIOLOGY; GENES, PLANT; GENOME, PLANT; GENOMICS; ORYZA SATIVA; SYNTENY; ZEA MAYS;

EID: 38949151064     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2007.03326.x     Document Type: Article

References (51)

1. Adams, K.L. Wendel, J.F. (2005) Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8, 135 141.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403 410.
3. Birchler, J.A., Riddle, N.C., Auger, D.L. Veitia, R.A. (2005) Dosage balance in gene regulation: biological implications. Trends Genet. 21, 219 226.
4. Bossolini, E., Wicker, T., Knobel, P.A. Keller, B. (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J. 49, 704 717.
5. Bowers, J.E., Chapman, B.A., Rong, J. Paterson, A.H. (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, 422, 433 438.
6. Bray, N., Dubchak, I. Pachter, L. (2003) AVID: a global alignment program. Genome Res. 13, 97 102.
7. Brudno, M. Morgenstern, B. (2002) Fast and sensitive alignment of large genomic sequences. Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB). IEEE Computer Society Press.
8. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., NISC Comparative Sequencing Program, Green, E.D., Sidow, A. Batzoglou, S. (2003a) LAGAN and Multi-Lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721 731.
9. Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I. Batzoglou, S. (2003b) Glocal alignment: finding rearrangements during alignment. Bioinformatics, 19 (Suppl. 1 I54 I62.
10. Couper, G.M., Singaravelu, S.A.G. Sidow, A. (2004) ABC: software for interactive browsing of genomic multiple sequence alignment data. BMC Bioinformatics, 5, 192.
11. De Bodt, S., Maere, S. Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591 597.
12. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L. Postlethwait, J. (1999) Preservation of duplicate gene by complementary degenerative mutations. Genetics, 151, 1531 45.
13. Freeling, M. (2007) The evolutionary position of subfunctionalization, downgraded. Genome Dyn., in press.
14. Freeling, M., Rapaka, L., Lyons, E., Pedersen, B. Thomas, B.C. (2007) G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell, 19, 1441 1457.
15. Freeling, M. Thomas, B.C. (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16, 805 814.
16. Gao, L.Z. Innan, H. (2004) Very low gene duplication rate in the yeast genome. Science, 306, 1367 1370.
17. Goode, D.K., Snell, P., Smith, S.F., Cooke, J.E. Elgar, G. (2005) Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3. Genomics, 86, 172 181.
18. Guo, H. Moose, S.P. (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell, 15, 1143 1158.
19. Haberer, G., Hindemitt, T., Meyers, B.C. Meyers, K.F. (2004) Trandscriptional similarities, dissimilarities and conservation of cis-acting elements in duplicated genes in Arabidopsis. Plant Physiol. 136, 3009 22.
20. Hardison, R.C. (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16, 369 372.
21. Hardison, R.C. (2003) Comparative Genomics. PLoS Biol. 1, E58.
22. Inada, D.C., A. Bashir, A., Lee, C., Thomas, B.C., Ko, C., Goff, S.A. Freeling, M. (2003) Conserved noncoding sequences in the grasses. Genome Res. 13, 2030 2041.
23. Jaillon, O., Aury, J., Noel, B. et al. (2007) The grapevine genome sequence suggests ancestral hexploidization in major angiosperm phyla. Nature, 449, 463 467.
24. Kaplinsky, N.J., Braun, D.M., Penterman, J., Goff, S.A. Freeling, M. (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc. Natl Acad. Sci. USA, 99, 6147 6151.
25. Koonin, E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39, 309 338.
26. Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A. Freeling, M. (2004) Genomic duplication, fractionation and the origin of regulatory novelty. Genetics, 166, 935 945.
27. Loots, G.G., Locksley, R.M., Blankespoor, C.M., Wang, Z.E., Miller, W., Rubin, E.M. Frazer, K.A. (2000) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science, 288, 136 140.
28. Ludwig, M.Z., Palsson, A., Alekseeva, E., Bergman, C.M., Nathan, J. Kreitman, M. (2005) Functional evolution of a cis-regulatory module. PLoS Biol. 3, e93.
29. Lynch, A. Force, A. (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics, 154, 459 73.
30. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L.S. Dubchak, I. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16, 1046 1047.
31. Mayr, E. (1993) What was the Evolutionary Synthesis? Trends Ecol. Evol. 8, 31 34.
32. Morgenstern, B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211 218.
33. Morgenstern, B., French, K., Dress, A. Werner, T. (1998) DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290 294.
34. Moses, A.M., Pollard, D.A., Nix, D.A., Iyer, V.N., Li, X.Y., Biggin, M.D. Eisen, M.B. (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput. Biol. 2, e130.
35. Needleman, S.B. Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443 453.
36. Ovcharenko, I., Loots, G.G., Giardine, B.M., Hou, M., Ma, J., Hardison, R.C., Stubbs, L. Miller, W. (2005a) Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15, 184 194.
37. Ovcharenko, I., Loots, G.G., Nobrega, M.A., Hardison, R.C., Miller, W. Stubbs, L. (2005b) Evolution and functional classification of vertebrate gene deserts. Genome Res. 15, 137 145.
38. Paterson, A.H., Bowers, J.E., Van de Peer, Y. Vandepoele, K. (2005) Ancient duplication of cereal genomes. New Phytol. 165, 658 661.
39. Pearson, H. (2006) Genetics: what is a gene? Nature, 441, 398 401.
40. Pohler, D., Werner, N., Steinkamp, R. Morgenstern, B. (2005) Multiple alignment of genomic sequences using CHAOS, DIALIGN, and ABC. Nucleic Acids Res. 33, 532 534.
41. Pollard, D., Bergman, C., Stoye, J., Celniker, S. Eisen, M. (2006) Benchmarking tools for the alignments of functional noncoding DNA. BMC Bioinformatics, 5, 6.
42. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R.C. Miller, W. (2000) PipMaker - a Web server for aligning two genomic DNA sequences. Genome Res. 10, 577 586.
43. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D Miller, W. (2003) Human-mouse alignments with blastz. Genome Res. 13, 103 107.
44. Siepel, A., Bejserano, G., Pedersen, J.S. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034 1050.
45. Smith, T.F. Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195 197.
46. Tatusova, T.A. Madden, T.L. (1999) blast 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174, 247 250.
47. Thomas, B.C., Pedersen, B. Freeling, M. (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16, 934 946.
48. Thomas, B.C., Rapaka, L., Lyons, E., Pedersen, B. Freeling, M. (2007) Intragenomic conserved noncoding sequences in Arabidopsis. Proc. Natl Acad. Sci. 104, 3348 3353.
49. Tuskan, G.A., Difazio, S., Jansson, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596 1604.
50. Wang, J., Tian, L., Lee, H.S. et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics, 172, 507 517.
51. Woolfe, A., Goodson, M., Goode, D.K. et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7.