Isolation of a family of resistance gene analogue sequences of the nucleotide binding site (NBS) type from Lens species

Genome

Volumn 47, Issue 4, 2004, Pages 650-659

  Yaish, M W F ^a,b   Saenz De Miera L E ^a   Perez De La Vega M ^a  

^a UNIVERSITY OF LEÓN   (Spain)

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Comparative analysis; Disease resistance genes; Lentils; LRR; TIR

Indexed keywords

NUCLEOTIDE; PLANT DNA; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; GENE; GENETIC POLYMORPHISM; GENETICS; LENTIL; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DISEASE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; LENS PLANT; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PHYLOGENY; PLANT DISEASES; PLANT PROTEINS; POLYMORPHISM, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID;

EMBRYOPHYTA; LENS CULINARIS; STAPHYLOCOCCUS PHAGE 3A;

EID: 5144223838     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G04-027     Document Type: Article

References (53)

1. Baker, B., Zambryski, P., Staskawicz, B., and Dinesh-Kumar, S.P. 1997. Signaling in plant-microbe interactions. Science (Washington, D.C.), 276: 726-733.
2. Bent, A.F. 1996. Plant disease resistance genes, function meets structure. Plant Cell, 8: 1757-1771.
3. Beroud, C., Antignac, C., Jeanpierre, C., and Junien, C. 1990. Un programme informatique pour la recherche d'amorces pour l'amplification par PCR. Med. Sci. 6: 901-903.
4. Boyle, J.S., and Lew, A.M. 1995. An inexpensive alternative to glassmilk for DNA purification. Trends Genet. 11: 8.
5. 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.
6. Chida, Y., Okazaki, K., Karasawa, A., Akashi, K., Nakazawa, S.H., Takahashi, H., and Ehara, Y. 2000. Isolation of molecular markers linked to the Cry locus conferring resistance to cucumber mosaic cucumovirus infection in cowpea. J. Gen. Plant Pathol. 66: 242-250.
7. Compton, T. 1990. Degenerate primers for DNA amplification. In PCR protocols, a guide to methods and applications. Edited by M.A. Innis, D.H. Gelfand, J.J. Sninsky, and T.J. White. Academic Press, London, UK. pp. 39-45.
8. Cordero, J.C., and Skinner, D.Z. 2002. Isolation from alfalfa of resistance gene analogues containing nucleotide binding sites. Theor. Appl. Genet. 104: 1283-1289.
9. Creusot, F., Macadré, C., Ferrier Cana, E., Riou, C., Geffroy, V., Sévignac, M., Dron, M., and Langin, T. 1999. Cloning and molecular characterization of three members of NBS-LRR subfamily located in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris. Genome, 42: 254-264.
10. Dayhoff, M.O. 1979. Atlas of protein sequences and structure. Vol. 5. Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
11. Dellaporta, S.L., Wood, J., and Hicks, J.B. 1983. A plant DNA minipreperation, version II. Plant MoI. Biol. 1: 19-21.
12. Di Gaspero, G., and Cipriani, G. 2002. Resistance gene analogs are candidate markers for disease-resistance genes in grape (Vitis spp.). Theor. Appl. Genet. 106: 163-172.
13. Dodds, P.N., Lawrence, G.J., and Ellis, J.G. 2001. Six amino acid changes confined to the leucine-rich repeat b-strand/b-turn motif determine the difference between the P and P2 rust resistance specificities in flax. Plant Cell, 13: 163-178.
14. Ellis, J., Dodds, P., and Pryor, T. 2000. Structure, function and evolution of plant disease resistance genes. Curr. Opin. Plant Biol. 3: 278-284.
15. Erskine, W., Bayaa, B., and Saxena, M.C. 1996. Registration of ILL5588 lentil germplasm resistant to vascular wilt and ascochyta blight. Crop Sci. 36: 1080.
16. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle, Wash.
17. Ferrier-Cana, E., Geoffroy, V., Macadré, C., Creusot, F., Imbert-Belloré, P., Sívingac, M., and Langing, T. 2003. Characterization of expressed NBS-LRR resistance gene candidates from common bean. Theor. Appl. Genet. 106: 251-261.
18. Fitch, W.M., and Margoliash, E. 1967. Construction of phylogenetic trees. Science (Washington, D.C.), 155: 279-284.
19. Forster, C., Arthur, E., Crespi, S., Hobbs, S.L.A., Mullineaux, P., and Casey, R. 1994. Isolation of a pea (Pisum sativum) seed lipoxygenase promoter by inverse polymerase chain reaction and characterization of its expression in transgenic tobacco. Plant Mol. Biol. 26: 235-248.
20. Geffroy, V., Creusot, F., Falquet, J., and Sévignac, M. 1998. A family of LRR sequences in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris and its potential use in marker-assisted selection. Theor. Appl. Genet. 96: 494-502.
21. Graham, M.A., Marek, L.F., Lohnes, D., Cregan, P., and Shoemaker, C. 2000. Expression and genome organization of resistance gene analogs in soybean. Genome, 43: 96-93.
22. 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 (Washington, D.C.), 269: 843-846.
23. Hammond-Kosack, K.E., and Jones, J.D.G. 1997. Plant disease resistance genes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 575-607.
24. Henikoff, S., and Henikoff, J. 1994. Protein family classification based on searching a database of blocks. Genomics, 19: 97-107.
25. Holmes, D.S., and Quigley, M. 1981. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114: 193-197.
26. Kanazin, V., Fredrick Marek, L., and Shoemaker, R.C. 1996. Resistance gene analogs are conserved and clustered in soybean. Proc. Natl. Acad. Sci. U.S.A. 93: 11 746 - 11 750.
27. Kawaoka, A., Kawamoto, T., Sekine, M., Yoshida, K., Takano, M., and Shinmyo, A. 1994. A cis-acting element and trans-acting factor involved in two wound-induced expression of horseradish peroxidase gene. Plant J. 6: 87-97.
28. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
29. Kobe, B., and Deisenhofer, J. 1994. The leucine-rich repeat, a versatile binding motif. Trends Biochem. Sci. 19: 415-421.
30. Korfhage, U., Trezzini, G.F., Meier, I., Hahlbrock, K., and Somssich, E. 1994. Plant homeodomain protein involved in transcriptional regulation of a pathogen defense-related gene. Plant Cell, 6: 695-708.
31. Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: molecular evolutionary genetics analysis software. Arizona State University, Tempe, Ariz.
32. Meyers, B.C., Chin, D.B., Shen, K.A., Sivaramakrishnan, S., Lavelle, D.O., Zhang, Z., and Michelmore, R.W. 1998. The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell, 10: 1817-1832.
33. 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.
34. Meyers, B.C., Kozik, A., Griego, A., Kuang, H.H., and Michelmore, R.W. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 15: 809-834.
35. Michelmore, R.W. 2000. Genomic approaches to plant disease resistance. Curr. Opin. Plant Biol. 3: 125-131.
36. Michelmore, R.W., and Meyers, B.C. 1998. Clusters of resistance genes in plants evolve by divergent selection and birth-and-death process. Genome Res. 8: 1113-1130.
37. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York, N.Y.
38. Nei, M., and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
39. Noël, L., Moorers, T.L., Van der Biezen, E.A., Parniske, M., Daniels, M.J., Parker, J.E., and Jones, J.D.G. 1999. Pronounced intraspecific haplotype divergence in the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell, 11: 2099-2111.
40. Noir, S., Combes, M.-C., Anthony, F., and Lashermes, P. 2001. Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee tree (Coffea L.). Mol. Genet. Genomics, 265: 654-662.
41. Pan, Q., Jonathan, W., and Fluhr, R. 2000. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50: 203-213.
42. Rivkin, M.I., Vallejos, C.E., and McClean, P.E. 1999. Disease-resistance related sequences in common bean. Genome, 42: 41-47.
43. Rozas, J., and Rozas, R. 1999. DnaSP version 3, an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15: 174-175.
44. Sanger, F., Nicklen, S., and Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 179: 1144-1147.
45. Shen, K.A., Meyers, B.C., Isalm-Faridi, M.N., Chin, D.B., Stelly, D.M., and Michelmore, R.W. 1998. Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. Mol. Plant-Microbe Interact. 11: 815-823.
46. Silver, J., and Keerikatte, V. 1989. Novel use of polymerase chain reaction to amplify cellular DNA adjacent to an integrated provirus. J. Virol. 63: 1924-1928.
47. Staskawicz, B.J., Ausubel, F.M., Baker, B.J., Ellis, J.G., and Jones, J.D.J. 1995. Molecular genetics of plant disease resistance. Science (Washington, D.C.), 268: 661-667.
48. 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: 4876-4782.
49. Traut, T.W. 1994. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur. J. Biochem. 222: 9-19.
50. Triglia, T., Peterson, M.G., and Kemp, D.J. 1988. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16: 8186.
51. Young, N.D. 2000. The genetic architecture of resistance. Curr. Opin. Plant Biol. 3: 285-290.
52. Yu, Y.G., Buss, G.R., and Saghai Maroof, M.A. 1996. Isolation of a superfamily of candidate disease resistance genes in soybean based on a conserved nucleotide-binding site. Proc. Natl. Acad. Sci. U.S.A. 93: 11 751-11 756.
53. Zhu, H., Cannon, S.B., Young, N.D., and Cook, D.R. 2002. Phylogeny and genomic organization of the TIR and Non-TIR NBS-LRR resistance gene family in Medicago truncatula. Mol. Plant-Microbe Interact. 15: 529-539.