Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose"

Genetics

Volumn 178, Issue 4, 2008, Pages 2081-2091

  Xu, Qiang ^a   Wen, Xiaopeng ^b   Deng, Xiuxin ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b GUIZHOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE;

ARTICLE; CHESTNUT ROSE; COMPARATIVE ANATOMY; CONTROLLED STUDY; DNA POLYMORPHISM; GENE AMPLIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC RECOMBINATION; GENETIC STABILITY; GENETIC VARIABILITY; GENOMICS; GENOTYPE; MEIOSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE BINDING SITE; PHYLOGENY; PLANT EVOLUTION; PRIORITY JOURNAL; PROGENY; PROTEIN DOMAIN; ROSE; TRANSPOSON; AMINO ACID SEQUENCE; BINDING SITE; CHROMOSOME MAP; CROP; CYTOLOGY; FRUIT; GENE; GENETIC SELECTION; GENETICS; GENOME; GENOMIC INSTABILITY; IMMUNOLOGY; INNATE IMMUNITY; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PLANT DISEASE;

ERYSIPHALES; ROSA ROXBURGHII;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; CHROMOSOME MAPPING; CROPS, AGRICULTURAL; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; FRUIT; GENES, PLANT; GENOME, PLANT; GENOMIC INSTABILITY; IMMUNITY, NATURAL; MEIOSIS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOTIDES; PHYLOGENY; PLANT DISEASES; ROSA; SELECTION (GENETICS);

EID: 45849112554     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.086421     Document Type: Article

References (61)

1. ASHFIELD, T., A. BOCIAN, D. HELD, A. D. HENK, L. F. MAREK et al., 2003 Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. Mol. Plant Microbe Interact. 16: 817-826.
2. BAI, J., L. A. PENNILL, J. NING, S. W. LEE, J. RAMALINGAM et al., 2002 Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res. 12: 1871-1884.
3. BAKKER, E. G., C. TOOMAJIAN, M. KREITMAN and J. BERGELSON, 2006 A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18: 1803-1818.
4. BERGELSON, J., M. KREITMAN, E. A. STAHL and D. TIAN, 2001 Evolutionary dynamics of plant R-genes. Science 292: 2281-2284.
5. CAICEDO, A. L., and B. A. SCHAAL, 2004 Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium. Proc. Natl. Acad. Sci. USA 101: 17444-17449.
6. CAICEDO, A. L., B. A. SCHAAL and B. N. KUNKEL, 1999 Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96: 302-306.
7. CALENGE, F., C. G. VAN DE LINDEN, E. VAN DE WEG, H. J. SCHOUTEN, G. VAN ARKEL et al., 2005 Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple. Theor. Appl. Genet. 110: 660-668.
8. CANNON, S. B., H. Y. ZHU, A. M. BAUMGARTEN, R. SPANGLER, G. MAY et al., 2002 Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene families. J. Mol. Evol. 54: 548-562.
9. CHISHOLM, S. T., G. COAKER, B. DAY and B. J. STASKAWICZ, 2006 Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124: 803-814.
10. COLLINS, N. C., C. A. WEBB, S. SEAH, J. G. ELLIS, S. H. HULBERT et al., 1998 The isolation and mapping of disease resistance gene analogs in maize. Mol. Plant Microbe Interact. 11: 968-978.
11. DANGL, J. L., and J. D. G. JONES, 2001 Plant pathogens and integrated defence responses to infection. Nature 411: 826-833.
12. DEYOUNG, B. J., and R. W. INNES, 2006 Plant NBS-LRR proteins in pathogen sensing and host defense. Nat. Immunol. 7: 1243-1249.
13. DONALD, T. M., F. PELLERONE, A. F. ADAM- BLONDON, A. BOUQUET, M. R. THOMAS et al., 2002 Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine. Theor. Appl. Genet. 101: 301-308.
14. FRIEDMAN, A. R., and B. J. BAKER, 2007 The evolution of resistance genes in multi-protein plant resistance systems. Curr. Opin. Genet. Dev. 17: 1-7.
15. GRANDBASTIEN, M. A., 1998 Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3: 181-187.
16. GRUBE, R. C., E. R. RADWANSKI and M. JAHN, 2000 Comparative genetics of disease resistance within the Solanaceae. Genetics 155: 873-887.
17. HAMMOND-KOSACK, K. E., and J. D. G. JONES, 1997 Plant disease resistance genes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 575-607.
18. HUMPHREY, W., A. DALKE and K. SCHULTEN, 1996 VMD: visual molecular dynamics. J. Mol. Graph. 14: 33-38.
19. JONES, J. D. G., and J. L. DANGL, 2006 The plant immune system. Nature 444: 323-329.
20. KANAZIN, V., L. F. MAREK and R. C. SHOEMAKER, 1996 Resistance gene analogs are conserved and clustered in soybean. Proc. Natl. Acad. Sci. USA 93: 11746-11750.
21. KU, H. M., T. VISION, J. LIU and S. D. TANKSLEY, 2000 Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA 97: 9121-9126.
22. KUANG, H., S. S. WOO, B. C. MEYERS, E. NEVO and R. W. MICHELMORE, 2004 Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell 16: 2870-2894.
23. KUANG, H., F. WEI, M. R. MARANO, U. WIRTZ, X. WANG et al., 2005 The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum. Plant J. 44: 37-51.
24. LEE, S. Y., J. S. SEO, M. RODRIGUEZ- LANETTY and D. H. LEE, 2003 Comparative analysis of superfamilies of NBS-encoding disease resistance gene analogs in cultivated and wild apple species. Mol. Genet. Genomics 269: 101-108.
25. LEISTER, D., 2004 Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends Genet. 20: 116-122.
26. LEISTER, D., J. KURTH, D. A. LAURIE, M. YANO, T. SASAKI et al., 1998 Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl. Acad. Sci. USA 95: 370-375.
27. LUCK, J. E., G. J. LAWRENCE, P. N. DODDS, K. W. SHEPHERD and J. G. ELLIS, 2000 Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination. Plant Cell 12: 1367-1378.
28. MA, Y. X., Y. ZHU and C. F. WANG, 1997 The aging retarding effect of 'Long-Life CiLi'. Mech. Ageing Dev. 96: 171-189.
29. MARTINEZ-ZAMORA, M. G., A. P. CASTAGNARO and J. C. DIAZ-RICCI, 2004 Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries. Mol. Genet. Genomics 272: 480-487.
30. MARTI-RENOM, M. A., A. STUART, A. FISER, R. SÁNCHEZ, F. MELO et al., 2000 Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29: 291-325.
31. MCDOWELL, J. M., and A. S. A. SIMON, 2006 Recent insights into R gene evolution. Mol. Plant Pathol. 7: 437-448.
32. MCHALE, L., X. TAN, P. KOEHL and R. W. MICHELMORE, 2006 Plant NBS-LRR proteins: adaptable guards. Genome Biol. 7: 212.
33. MEER, J., R. CUDMORE and K. F. MANLY, 2004 Map Manager QTX. http://www.mapmanager.org/mmQTX.html
34. MEYERS, B. C., A. W. DICKERMAN, R. W. MICHELMORE, S. SIVARAMAKRISHNAN, B. W. SOBRAL et al., 1999 Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 20: 317-332.
35. MEYERS, B. C., A. KOZIK, A. GRIEGO, H. KUANG and R. W. MICHELMORE, 2003 Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809-834.
36. MICHELMORE, R. W., and B. C. MEYERS, 1998 Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8: 1113-1130.
37. MONDRAGON-PALOMINO, M., and B. S. GAUT, 2005 Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol. Biol. Evol. 22: 2444-2456.
38. MONDRAGON-PALOMINO, M., B. C. MEYERS, R. W. MICHELMORE and B. S. GAUT, 2002 Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 12: 1305-1315.
39. PAN, Q., Y. S. LIU, O. BUDAI-HADRIAN, M. SELA, L. CARMEL-GOREN et al., 2000a Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and Arabidopsis. Genetics 155: 309-322.
40. PAN, Q., J. WENDEL and R. FLUHR, 2000b Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J. Mol. Evol. 50: 203-213.
41. PLOCIK, A., J. LAYDEN and R. KESSELI, 2004 Comparative analysis of NBS domain sequences of NBS-LRR disease resistance genes from sunflower, lettuce, and chicory. Mol. Phylogenet. Evol. 31: 153-163.
42. RICHLY, E., J. KURTH and D. LEISTER, 2002 Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol. Biol. Evol. 19: 76-84.
43. RITTER, E., C. GEBHARDT and F. SALAMINI, 1990 Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125: 645-654.
44. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual, Ed. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
45. SHEN, K. A., B. S. MEYERS, M. N. ISLAM- FARIDI, D. B. CHIN, D. M. STELLY et al., 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. SMITH, S. M., and S. H. HULBERT, 2005 Recombination events generating a novel Rp1 race specificity. Mol. Plant Microbe Interact. 18: 220-228.
47. SONG, W. Y., L. Y. PI, T. E. BUREAU and P. C. RONALD, 1998 Identification and characterization of 14 transponson-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice. Mol. Gen. Genet. 258: 449-456.
48. SUDUPAK, M. A., J. L. BENNETZEN and S. H. HULBERT, 1993 Unequal exchange and meiotic instability of disease-resistance genes in the Rp1 region of maize. Genetics 133: 119-125.
49. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN and D. G. HIGGINS, 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4882.
50. TIAN, D., H. ARAKI, E. STAHL, J. BERGELSON and M. KREITMAN, 2002 Signature of balancing selection in Arabidopsis. Proc. Natl. Acad. Sci. USA 99: 11525-11530.
51. TIFFIN, P., 2004 Comparative evolutionary histories of chitinase genes in the genus Zea and family Poaceae. Genetics 167: 1331-1340.
52. WELTER, L. J., N. GOKTURK-BAYDAR, M. AKKURT, E. MAUL, R. EIBACH et al., 2007 Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L). Mol. Breed. 20: 359-374.
53. WEN, X. P., and X. X. DENG, 2005 Micropropagation of chestnut rose (Rosa roxburghii Tratt) and genetic stability assessment of the in vitro plants using RAPD and AFLP markers. J. Hortic. Sci. Biotechnol. 80: 54-60.
54. XIAO, S., B. EMERSON, K. RATANASUT, E. PATRICK, C. O'NEILL et al., 2004 Origin and maintenance of a broad-spectrum disease resistance locus in Arabidopsis. Mol. Biol. Evol. 21: 1661-1672.
55. XU, Q., X. P. WEN and X. X. DENG, 2005 Isolation of TIR and non-TIR NBS-LRR resistance gene analogues and identification of molecular markers linked to a powdery mildew resistance locus in chestnut rose (Rosa roxburghii Tratt). Theor. Appl. Genet. 111: 819-830.
56. XU, Q., X. P. WEN and X. X. DENG, 2007 Phylogenetic and evolutionary analysis of NBS-encoding genes in Rosaceae fruit crops. Mol. Phylogenet. Evol. 44: 315-324.
57. YANG, Z., 1997 PAML: A program package for phylogenetic analysis by maximum likehood. Comput. Appl. Biosci. 13: 555-556.
58. YANG, Z., R. NIELSEN, N. GOLDMAN and A. M. K. PEDERSEN, 2000 Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
59. YOUNG, N. D., 2000 The genetic architecture of resistance. Curr. Opin. Plant Biol. 3: 285-290.
60. YU, Y. G., G. R. BUSS and M. A. MAROOF, 1996 Isolation of a super-family of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc. Natl. Acad. Sci. USA 93: 11751-11756.
61. ZHU, H., S. B. CANNON, N. D. YOUNG and D. R. COOK, 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.