35S De Novo Methylation 28. Turker MS (2002) Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene 21: 5388–5393. 29. Kanazawa A, O’Dell M, Hellems RP (2007) The binding of nuclear factors to the as-1 element in the CaMV 35S promoter in affected by cytosine methylation in vitro. Plant Biol 9: 435–441. 30. Schubert D, Lechtenberg B, Forsbach A, Gils M, Bahadur S, et al. (2004) Silencing in Arabidopsis T-DNA transformants: The predominant role of a gene-specific RNA sensing mechanism versus position effects. Plant Cell 16: 2561–2572. 31. Nagaya S, Kato K, Ninomiya Y, Horie R, Sekine M, et al. (2005) Expression of randomly integrated single copy transgenes does not vary in Arabidopsis thaliana. Plant Cell Physiol 46: 438–444. 32. Stoger E, Ma JKC, Fischer R, Christou P (2005) Sowing the seeds of success: pharmaceutical proteins from plants. Curr Opin Plant Biotech 16: 167–173. 33. Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6: 271–282. 34. Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, et al. (2002) Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol 129: 13–22. 35. Annadana S, Mlyna´rova´ L, Udayakumar M, de Jong J, Nap JP (2001) The potato Lhca3.St.1 promoter confers high and stable transgene expression in chrysanthemum, in contrast to CaMV-based promoters. Mol Breed 8: 335–344. 36. McCabe MS, Schepers F, van der Arend A, Mohapatra U, de Laat AMM, et al. (1999) Increased stable inheritance of herbicide resistance in transgenic lettuce carrying a petE promoter-bar gene compared with a CaMV 35S-bar gene. Theor Appl Genet 99: 587–592. 37. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351–360. 38. Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89–97. 39. Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, et al. (2009) An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 28: 1078–1086. 40. Mishiba KI, Yamane K, Nakatsuka T, Nakano Y, Yamamura S, et al. (2009) Genetic relationships in the genus Gentiana based on chloroplast DNA sequence data and nuclear DNA content. Breed Sci 59: 119–127. 41. Narayan RKJ (1987) Nuclear DNA changes, genome differentiation and evolution in Nicotiana (Solanaceae). Plant Syst Evol 157: 161–180. 42. Mette MF, Kanno T, Aufsatz W, Jakowitsch J, van der Winden J, et al. (2002) Endogenous viral sequences and their potential contribution to heritable virus resistance in plants. EMBO J 21: 461–469. 43. Igasaki T, Ishida Y, Mohri T, Ichikawa H, Shinohara K (2002) Transformation of Populus alba and direct selection of transformants with the herbicide bialaphos. Bull FFPRI 1: 235–240. 44. Niwa Y, Hirano T, Yoshimoto K, Shimizu M, Kobayashi H (1999) Non- invasive quantitative detection and applications of non-toxic, S65T-type green fluorescent protein in living plants. Plant J 18: 455–463. 45. Thompson CJ, Movva NR, Tizard R, Crameri R, Davies JE, et al. (1987) Characterization of the herbicide-resistance gene bar from Streptomyces hygro- scopicus. EMBO J 6: 2519–2523. 46. Hood EE, Helmer GL, Fraley RT, Chilton MD (1986) The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T- DNA. J Bacteriol 168: 1291–1301. PLoS ONE | www.plosone.org 11 March 2010 | Volume 5 | Issue 3 | e9670