SEARCH

SEARCH BY CITATION

References

  • Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 33893402.
  • Bennett, M.D. and Smith, J.B. (1976) Nuclear DNA amounts in angiosperms. Phil. Trans. R. Soc. Lond. B, 274, 227274.
  • Bennetzen, J.L. (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell, 12, 10211030.
  • Bennetzen, J.L. and Ma, J. (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr. Opin. Plant Biol. 6, 128133.
  • Bennetzen, J.L., Coleman, C., Liu, R., Ma, J. and Ramakrishna, W. (2004) Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7, 732736.
  • Bossolini, E., Krattinger, S.G. and Keller, B. (2006) Development of SSR markers specific for the Lr34 resistance region of wheat using sequence information from rice and Aegilops tauschii. Theor. Appl. Genet. 113, 10491062.
  • Bruggmann, R., Bharti, A.K., Gundlach, H. et al. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16, 12411251.
  • Catalan, P. and Olmstead, R.G. (2000) Phylogenetic reconstruction of the genus Brachypodium P. Beauv. (Poaceae) from combined sequences of chloroplast ndhF gene and nuclear ITS. Plant Syst. Evol., 220, 119.
  • Chantret, N., Cenci, A., Sabot, F., Anderson, O. and Dubcovsky, J. (2004) Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol. Genet. Genom. 271, 377386.
  • Draper, J., Mur, L.A.J., Jenkins, G., Ghosh-Biswas, G.C., Bablak, P., Hasterok, R. and Routledge, A.P.M. (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127, 15391555.
  • Du, C., Swigonova, Z. and Messing, J. (2006) Retrotranspositions in orthologous regions of closely related grass species. BMC Evol. Biol. 6, 62.
  • Dubcovsky, J., Ramakrishna, W., SanMiguel, P.J., Busso, C.S., Yan, L.L., Shiloff, B.A. and Bennetzen, J.L. (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol. 125, 13421353.
  • Ewing, B., Hillier, L., Wendl, M.C. and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175185.
  • Feuillet, C. and Keller, B. (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. 89, 310.
  • Feuillet, C., Penger, A., Gellner, K., Mast, A. and Keller, B. (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, 13041313.
  • Foote, T., Griffiths, S., Allouis, S. and Moore, G. (2004) Construction and analysis of a BAC library in the grass Brachypodium sylvaticum and its use as a tool to bridge the gap between rice and wheat in elucidating gene content. Funct. Integr. Genomics, 4, 2633.
  • Gale, M.D. and Devos, K.M. (1998) Comparative genetics in the grasses. Proc. Natl Acad. Sci. USA, 95, 19711974.
  • Gallego, F., Feuillet, C., Messmer, M., Penger, A., Graner, A., Yano, M., Sasaki, T. and Keller, B. (1998) Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome, 41, 328336.
  • Griffiths, S., Sharp, R., Foote, T.N., Bertin, I., Wanous, M., Reader, S., Colas, I. and Moore, G. (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature, 439, 749752.
  • Gu, Y., Huo, N., Vogel, J., Garvin, D., Lazo, G. and Anderson, O. (2006) Construction and characterization of two BAC Libraries for Brachypodium distachyon, a new model for grass genomics. In Plant & Animal Genomes XIV Conference, San Diego, CA, USA, January 2006, http://www.Intl-pag.org/14/abstracts/PAG14_P58.html.
  • Guyot, R. and Keller, B., (2004) Ancestral genome duplication in rice. Genome, 47, 610614.
  • Hasterok, R., Marasek, A., Donnison, I.S., Armstead, I., Thomas, A., King, I.P., Wolny, E., Idziak, D., Draper, J. and Jenkins, G. (2006) Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics, 173, 349362.
  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793800.
  • Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. and Wessler, S.R. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431, 569573.
  • Kaplinsky, N.J., Braun, D.M., Penterman, J., Goff, S.A. and Freeling, M. (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc. Natl Acad. Sci. USA, 99, 61476151.
  • Katari, M.S., Balija, V., Wilson, R.K., Martienssen, R.A. and McCombie, W.R. (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res. 15, 496504.
  • Lai, J., Li, Y., Messing, J. and Dooner, H.K. (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl Acad. Sci. USA, 102, 90689073.
  • Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daley, M.J., Lincoln, S.E. and Newburg, L. (1987) mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1, 174181.
  • Leister, D., Kurth, J., Laurie, D.A., Yano, M., Sasaki, T., Devos, K., Graner, A. and Schulze-Lefert, P. (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl Acad. Sci. USA, 95, 370375.
  • Ma, J., SanMiguel, P., Lai, J., Messing, J. and Bennetzen, J.L. (2005) DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics, 170, 12091220.
  • Messing, J. and Llaca, V. (1998) Importance of anchor genomes for any plant genome project. Proc. Natl Acad. Sci. USA, 95, 20172020.
  • Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A. and Rafalski, A. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nature Genet. 37, 9971002.
  • Paillard, S., Schnurbusch, T., Winzeler, M., Messmer, M., Sourdille, P., Abderhalden, O., Keller, B. and Schachermayr, G. (2003) An integrative genetic linkage map of winter wheat (Triticum aestivum L.). Theor. Appl. Genet. 107, 12351242.
  • Paterson, A.H., Bowers, J.E. and Chapman, B.A. (2004) Ancient polyploidization predating divergence of the cereals and its consequences for comparative genomics. Proc. Natl Acad. Sci. USA, 101, 99039908.
  • SanMiguel, P.J., Ramakrishna, W., Bennetzen, J.L., Busso, C. and Dubcovsky, J. (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5. Am. Funct. Integr. Genomics, 2, 7080.
  • Schnurbusch, T., Paillard, S., Schori, A., Messmer, M., Schachermayr, G., Winzeler, M. and Keller, B. (2004) Dissection of quantitative and durable leaf rust resistance in Swiss winter wheat reveals a major resistance QTL in the Lr34 chromosomal region. Theor. Appl. Genet. 108, 477484.
  • Song, R., Llaca, V. and Messing, J. (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res. 12, 15491555.
  • Sonnhammer, E.L. and Durbin, R. (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 167, 110.
  • Stein, N., Feuillet, C., Wicker, T., Schlagenhauf, E. and Keller, B. (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, 1343613441.
  • Swigonova, Z., Bennetzen, J.L. and Messing, J. (2005) Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum. Genetics, 169, 891906.
  • 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, 381391.
  • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) ClustalW, improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 46734680.
  • Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Laudencia-Chingcuanco, D., Hayden, D.M., Donze, T.J., Vivian, L.A., Stamova, B. and Coleman-Derr, D. (2006) EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor. Appl. Genet. 113, 186195.
  • Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E. and Keller, B. (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26, 307316.
  • Wicker, T., Guyot, R., Yahiaoui, N. and Keller, B. (2003a) CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol. 132, 5263.
  • Wicker, T., Yahiaoui, N., Guyot, R., Schlagenhauf, E., Liu, Z.-D., Dubcovsky, J. and Keller, B. (2003b) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell, 15, 11861197.
  • Wolfe, K.H., Gouy, M.L., Yang, Y.W., Sharp, P.M. and Li, W.H. (1989) Date of the monocot–dicot divergence estimated from chloroplast DNA-sequence data. Proc. Natl Acad. Sci. USA, 86, 62016205.