Diversification of non-TIR class NB-LRR genes in relation to whole-genome duplication events in Arabidopsis

Molecular Plant-Microbe Interactions

Volumn 18, Issue 2, 2005, Pages 103-109

  Nobuta, Kan ^a   Ashfield, Tom ^a   Kim, Sun ^b   Innes, Roger W ^a  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; GENE; GENE DUPLICATION; GENETIC VARIABILITY; GENETICS; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; GENOME, PLANT; LEUCINE; MULTIGENE FAMILY; PHYLOGENY; PLANT PROTEINS; REPETITIVE SEQUENCES, AMINO ACID; VARIATION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 12444288067     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI-18-0103     Document Type: Article

References (45)

1. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
2. Ashfield, T., Ong, L. E., Nobuta, K., Schneider, C. M., and Innes, R. W. 2004. Convergent evolution of disease resistance gene specificity in two flowering plant families. Plant Cell 16:309-318.
3. Barkan, A., Walker, M., Nolasco, M., and Johnson, D. 1994. A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO (Eur. Mol. Biol. Organ.) J. 13:3170-3181.
4. Baumgarten, A., Cannon, S., Spangler, R., and May, G. 2003. Genome-level evolution of resistance genes in Arabidopsis thaliana. Genetics 165:309-319.
5. Bent, A. F., Kunkel, B. N., Dahlbeck, D., Brown, K. L., Schmidt, R., Giraudat, J., Leung, J., and Staskawicz, B. J. 1994. RPS2 of Arabidopsis thaliana: A leucine-rich repeat class of plant disease resistance genes. Science 265:1856-1860.
6. Blanc, G., and Wolfe, K. H. 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691.
7. Blanc, G., Hokamp, K., and Wolfe, K. H. 2003. A recent polyploidy super-imposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13:137-144.
8. Bowers, J. E., Chapman, B. A., Rong, J., and Paterson, A. H. 2003. Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.
9. Cannon, S. B., Mitra, A., Andrew, B., Young, N. D., and May, G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 4:10.
10. Cannon, S. B., Zhu, H., Baumgarten, A. M., Spangler, R., May, G., Cook, D. R., and Young, N. D. 2002. Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. J. Mol. Evol. 54:548-562.
11. Collins, N., Drake, J., Ayliffe, M., Sun, Q., Ellis, J., Hulbert, S., and Pryor, T. 1999. Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants. Plant Cell 11:1365-1376.
12. Conery, J. S., and Lynch, M. 2001. Nucleotide substitutions and the evolution of duplicate genes. Pacific Symposium of Biocomputing 6:167-178.
13. Dangl, J. L., and Jones, J. D. 2001. Plant pathogens and integrated defence responses to infection. Nature 411:826-833.
14. Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y.-I., and Postlethwait, J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
15. Grant, M. R., Godiard, L., Straube, E., Ashfield, T., Lewald, J., Sattler, A., Innes, R. W., and Dangl, J. L. 1995. Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269:843-846.
16. Huelsenbeck, J. P., and Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
17. Hulbert, S. H., Webb, C. A., Smith, S. M., and Sun, Q. 2001. Resistance gene complexes: Evolution and utilization. Annu. Rev. Phytopathol. 39:285-312.
18. Kashkush, K., Feldman, M., and Levy, A. A. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651-1659.
19. Leister, D. 2004. Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends Genet. 20:116-122.
20. Lynch, M., and Conery, J. S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
21. Lynch, M., and Force, A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
22. Manthey, G. M., and McEwen, J. E. 1995. The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae. EMBO (Eur. Mol. Biol. Organ.) J. 14:4031-4043.
23. McDowell, J. M., Dhandaydham, M., Long, T. A., Aarts, M. G., Goff, S., Holub, E. B., and Dangl, J. L. 1998. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10:1861-1874.
24. Meyers, B. C., Dickerman, A. W., Michelmore, R. W., Sivaramakrishnan, S., Sobral, B. W., and Young, N. D. 1999. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 20:317-332.
25. Meyers, B. C., Morgante, M., and Michelmore, R. W. 2002. TIR-X and TIR-NBS proteins: Two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J. 32:77-92.
26. Meyers, B. C., Kozik, A., Griego, A., Kuang, H., and Michelmore, R. W. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15:809-834.
27. Mino, M., Maekawa, K., Ogawa, K., Yamagishi, H., and Inoue, M. 2002. Cell death processes during expression of hybrid lethality in interspecific F(1) hybrid between Nicotiana gossei Domin and Nicotiana tabacum. Plant Physiol. 130:1776-1787.
28. Nei, M., and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
29. Noel, L., Moores, T. L., van Der Biezen, E. A., Parniske, M., Daniels, M. J., Parker, J. E., and Jones, J. D. 1999. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099-2112.
30. Ozkan, H., Levy, A. A., and Feldman, M. 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13:1725-1747.
31. Pan, Q., Wendel, J., and Fluhr, R. 2000. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50:203-213.
32. Parniske, M., Hammond-Kosack, K. E., Golstein, C., Thomas, C. M., Jones, D. A., Harrison, K., Wulff, B. B., and Jones, J. D. 1997. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91:821-832.
33. Richly, E., Kurth, J., and Leister, D. 2002. Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol. Biol. Evol. 19:76-84.
34. Sidow, A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6:715-722.
35. Simillion, C., Vandepoele, K., Van Montagu, M. C., Zabeau, M., and Van de Peer, Y. 2002. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 99:13627-13632.
36. Stoltzfus, A. 1999. On the possibility of constructive neutral evolution. J. Mol. Evol. 49:169-181.
37. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
38. Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
39. Tian, D., Traw, M. B., Chen, J. Q., Kreitman, M., and Bergelson, J. 2003. Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature 423:74-77.
40. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., and Van De Peer, Y. 2002. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12:1792-1801.
41. Vision, T. J., Brown, D. G., and Tanksley, S. D. 2000. The origins of genomic duplications in Arabidopsis. Science 290:2114-2117.
42. Warren, R. F., Henk, A., Mowery, P., Holub, E., and Innes, R. W. 1998. A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes. Plant Cell 10:1439-1452.
43. Flanders Interuniversity Institute for Biotechnology and Ghent University Plant Systems Biology webpage: www.psb.rug.ac.be
44. Genetics Department, Trinity College Dublin, Ken Wolfe's lab site for paralogons in Arabidopsis thaliana: wolfe.gen.tcd.ie/athal/dup
45. The Institute for Genomic Research (TIGR) Arabidopsis thaliana disease resistance gene resource: www.tigr.org/tdb/e2k1/ath1/disRgenes.shtml.