| 
                                                    1                                                 | 
                                                
                                                     Whitelam, G. C., Johnson, E., Peng, J., Carol, P., Anderson, M. L., Cowl, J. S., et al.  (1993). Phytochrome A null mutants of Arabidopsis display a wild-type phenotype  in white light. Plant Cell 5, 757–768. doi: 10.1105/tpc.5.7.757                                                  | 
                                            
                                                                                    
                                                | 
                                                    2                                                 | 
                                                
                                                    Desnos,  T.,  Puente,  P.,  Whitelam,  G.  C.,  and  Harberd,  N.  P.  (2001).  FHY1:  aphytochrome  A-specific  signal  transducer.  Genes  Dev.  15,  2980–2990.  doi:  10.1101/gad.205401                                                  | 
                                            
                                                                                    
                                                | 
                                                    3                                                 | 
                                                
                                                    Hiltbrunner,  A.,  Viczian,  A.,  Bury,  E.,  Tscheuschler,  A.,  Kircher,  S.,  Toth,  R.,  et  al.(2005).  Nuclear  accumulation  of  the  phytochrome  A  photoreceptor  requires  FHY1. Curr. Biol. 15, 2125–2130. doi: 10.1016/j.cub.2005.10.042                                                  | 
                                            
                                                                                    
                                                | 
                                                    4                                                 | 
                                                
                                                    Zhou, Q.,Hare, P. D., Yang, S. W., Zeidler, M., Huang, L. F., and Chua, N. H. (2005).  FHL is required for full phytochrome A signaling and shares overlapping functions  with FHY1. Plant J. 43, 356–370. doi: 10.1111/j.1365-313X.2005.02453.x                                                  | 
                                            
                                                                                    
                                                | 
                                                    5                                                 | 
                                                
                                                    Hudson, M.,  Ringli,  C.,  Boylan, M.  T.,  and  Quail,  P.  H.  (1999).  The  FAR1  locus  encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev.13,  2017–2027. doi: 10.1101/gad.13.15.2017                                                 | 
                                            
                                                                                    
                                                | 
                                                    6                                                 | 
                                                
                                                    Wang, H., and Deng, X. W. (2002). Arabidopsis FHY3 defines a key phytochrome A  signaling component directly interacting with its homologous partner FAR1. EMBO  J. 21, 1339–1349. doi: 10.1093/emboj/21.6.1339                                                  | 
                                            
                                                                                    
                                                | 
                                                    7                                                 | 
                                                
                                                    Lin,  R.,  Ding,  L.,  Casola,  C.,  Ripoll,  D.  R.,  Feschotte,  C.,  and Wang,  H.  (2007).  Transposase-derived  transcription  factors  regulate  light  signaling  in Arabidopsis.  Science 318, 1302–1305. doi: 10.1126/science.1146281                                                 | 
                                            
                                                                                    
                                                | 
                                                    8                                                 | 
                                                
                                                    Lin,  R.,  and Wang, H.  (2004).  Arabidopsis  FHY3/FAR1  gene  family  and  distinct  roles of its members in light control of Arabidopsis development. Plant Physiol.136,  4010–4022. doi: 10.1104/pp.104.052191                                                 | 
                                            
                                                                                    
                                                | 
                                                    9                                                 | 
                                                
                                                    Aguilar-Martinez, J. A., Uchida, N., Townsley, B., West, D. A., Yanez, A., Lynn, N.,  et al. (2015). Transcriptional, posttranscriptional, and posttranslational regulation of  SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function  in the shoot apex. Plant Physiol. 167, 424–442.doi: 10.1104/pp.114.248625                                                  | 
                                            
                                                                                    
                                                | 
                                                    10                                                 | 
                                                
                                                     Li, G., Siddiqui, H., Teng, Y., Lin, R., Wan, X. Y., Li,  J.,  et  al.  (2011). Coordinated  transcriptional  regulation underlying  the  circadian  clock  in Arabidopsis. Nat.Cell  Biol. 13, 616–622. doi: 10.1038/ncb2219                                                  | 
                                            
                                                                                    
                                                | 
                                                    11                                                 | 
                                                
                                                     Joly-Lopez,  Z.,  and  Bureau,  T.  E.  (2014). Diversity  and  evolution  of  transposable  elements  in Arabidopsis.  Chromosome  Res.  22,  203–216.  doi:  10.1007/s10577-014- 9418-8                                                  | 
                                            
                                                                                    
                                                | 
                                                    12                                                 | 
                                                
                                                     Feschotte, C., Jiang, N., and Wessler, S. R. (2002). Plant transposable elements:where  genetics meets genomics. Nat. Rev. Genet. 3, 329–341. doi: 10.1038/nrg793                                                  | 
                                            
                                                                                    
                                                | 
                                                    13                                                 | 
                                                
                                                     Makarova, K. S., Aravind, L., and Koonin, E. V. (2002). SWIM, a novel Zn-chelating  domain present  in bacteria, archaea and  eukaryotes. Trends Biochem. Sci. 27,384– 386. doi: 10.1016/S0968-0004(02)02140-0                                                 |