Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Proceedings of the National Academy of Sciences of the United States of America

Volumn 104, Issue 29, 2007, Pages 12057-12062

  Borevitz, Justin O ^a,c   Hazen, Samuel P ^d   Michael, Todd P ^a   Morris, Geoffrey P ^c   Baxter, Ivan R ^e   Hu, Tina T ^f   Chen, Huaming ^a   Werner, Jonathan D ^a   Nordborg, Magnus ^f   Salt, David E ^e   Kay, Steve A ^d   Chory, Joanne ^a,b   Weigel, Detlef ^a,g   Jones, Jonathan D G ^h   Ecker, Joseph R ^a  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

^e PURDUE UNIVERSITY   (United States)

^f UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^g MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^h SAINSBURY LABORATORY   (United Kingdom)

Author keywords

Evolutionary genomics; Gene array; Nucleotide diversity

Indexed keywords

F BOX PROTEIN; HELIX LOOP HELIX PROTEIN; UBIQUITIN PROTEIN LIGASE;

ARABIDOPSIS; ARTICLE; CENTROMERE; DISEASE RESISTANCE; EVOLUTION; GENE EXPRESSION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; GENOMICS; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; SINGLE FEATURE POLYMORPHISM;

ARABIDOPSIS; CHROMOSOMES, PLANT; GENES, PLANT; GENOME, PLANT; HAPLOTYPES; POLYMORPHISM, GENETIC; SELECTION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 34547549855     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0705323104     Document Type: Article

References (57)

1. Toomajian C, Hu TT, Aranzana MJ, Lister C, Tang C, Zheng H, Zhao K, Calabrese P, Dean C, Nordborg M (2006) PLoS Biol 4:e137.
2. Yoshida K, Kamiya T, Kawabe A, Miyashita NT (2003) Genes Genet Syst 78:11-21.
3. Miyashita NT, Kawabe A, Innan H (1999) Genetics 152:1723-1731.
4. Sharbel TF, Haubold B, Mitchell-Olds T (2000) Mol Ecol 9:2109-2118.
5. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, et al. (2002) Nat Genet 30:190-193.
6. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, et al. (2005) PLoS Biol 3:e196.
7. Schmid KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T (2005) Genetics 169:1601-1615.
8. Borevitz JO, Chory J (2004) Curr Opin Plant Biol 7:132-136.
9. Hazen SP, Kay SA (2003) Trends Plants Sci 8:413-416.
10. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, et al. (1998) Science 281:1194-1197.
11. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Genome Res 13:513-523.
12. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT (2007) PLoS ONE 2:e284.
13. Turner TL, Hahn MW, Nuzhdin SV (2005) PLoS Biol 3:e285.
14. Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch K, Sarr O, Ndir O, Mboup S, et al. (2006) PLoS Pathogenet 2:e57.
15. Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R (2005) Genome Biol 6:R54.
16. Cui X, Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, Close TJ (2005) Bioinformatics 21:3852-3858.
17. Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA (2005) Plant Physiol 138:990-997.
18. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005) Proc Natl Acad Sci USA 102:10387-10392.
19. Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E, Salt DE (2006) PLoS Genet 2:e210.
20. Werner JD, Borevitz JO, Uhlenhaut H, Ecker JR, Chory J, Weigel D (2005) Genetics 170:1197-1207.
21. Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker JR, Chory J, Weigel D (2005) Proc Natl Acad Sci USA 102:2460-2465.
22. Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J (2004) Genetics 167:907-917.
23. Jiang R, Marjoram P, Borevitz JO, Tavare S (2006) Genetics 173:2257-2267.
24. Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, et al. (2007) Proc Natl Acad Sci USA 104:2271-2276.
25. Kim S, Zhao K, Jiang R, Molitor J, Borevitz JO, Nordborg M, Marjoram P (2006) Genetics 173:1125-1133.
26. Borevitz J (2006) Methods Mol Biol 323:137-145.
27. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) Bioinformatics 19:185-193.
28. Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L (2005) Genome Res 15:284-291.
29. Naef F, Lim DA, Patil N, Magnasco M (2002) Phys Rev E 65:040902.
30. Tajima F (1989) Genetics 123:585-595.
31. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH (2000) Cell 100:367-376.
32. Arabidopsis Genome Initiative (2000) Nature 408:796-815.
33. Singer T, Fan Y, Chang HS, Zhu T, Hazen SP, Briggs SP (2006) PLoS Genet 2:e144.
34. Hellmann I, Ebersberger I, Ptak SE, Paabo S, Przeworski M (2003) Am J Hum Genet 72:1527-1535.
35. Wright SI, Foxe JP, DeRose-Wilson L, Kawabe A, Looseley M, Gaut BS, Charlesworth D (2006) Genetics 174:1421-1430.
36. Takahashi A, Liu YH, Saitou N (2004) Mol Biol Evol 21:404-409.
37. Gassmann W, Hinsch ME, Staskawicz BJ (1999) Plant J 20:265-277.
38. Nasrallah ME, Liu P, Nasrallah JB (2002) Science 297:247-249.
39. Igic B, Kohn JR (2001) Proc Natl Acad Sci USA 98:13167-13171.
40. Liu P, Sherman-Broyles S, Nasrallah ME, Nasrallah JB (2007) Curr Biol 17:734-740.
41. Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Plant Cell 15:809-834.
42. Fritz-Laylin LK, Krishnamurthy N, Tor M, Sjolander KV, Jones JD (2005) Plant Physiol 138:611-623.
43. Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH (2004) Plant Cell 16:1220-1234.
44. Shiu SH, Bleecker AB (2003) Plant Physiol 132:530-543.
45. Mondragon-Palomino M, Meyers BC, Michelmore RW, Gaut BS (2002) Genome Res 12:1305-1315.
46. Mauricio R, Stahl EA, Korves T, Tian D, Kreitman M, Bergelson J (2003) Genetics 163:735-746.
47. Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J (1999) Nature 400:667-671.
48. Tian DC, Araki H, Stahl E, Bergelson J, Kreitman M (2002) Proc Natl Acad Sci USA 99:11525-11530.
49. Tian D, Traw MB, Chen JQ, Kreitman M, Bergelson J (2003) Nature 423:74-77.
50. Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Science 292:2281-2285.
51. Bakker EG, Toomajian C, Kreitman M, Bergelson J (2006) Plant Cell 18:1803-1818.
52. Bailey PC, Martin C, Toledo-Ortiz G, Quail PH, Huq E, Heim MA, Jakoby M, Werber M, Weisshaar B (2003) Plant Cell 15:2497-2502.
53. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, Callis J (2005) Plant Physiol 137:13-30.
54. Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD (2002) Proc Natl Acad Sci USA 99:11519-11524.
55. Zhang X, Richards EJ, Borevitz JO (2007) Curr Opin Plant Biol 10:142-148.
56. Watterson GA (1975) Theor Popul Biol 7:256-276.
57. Tajima F (1983) Genetics 105:437-460.