*4.2. Dof Gene Identification and Characterization*

To identify all the possible *Dof* genes in physic nut, both local BLASTP [40] and Hidden Markov model (HMM) searches were performed [41]. For BLASTP, the known Dof proteins from Arabidposis were taken as queries and the *<sup>E</sup>*-value was set to 1 <sup>×</sup> <sup>10</sup>−10. For the HMM search, the HMM profile of the Dof domain was used as query and the *E*-value was set to 1 [24]. All the retrieved sequences were further scanned and tested using SMART (Available online: http://smart.embl-heidelberg.de/) [42] and NCBI Conserved Domains database (Available online: http://www.ncbi.nih.gov/Structure/cdd/ cdd.shtml) for authentication of the presence of Dof domain [43]. We manually removed redundant sequences that do not have Dof domain or have incomplete encoding frame. Parameters, such as protein length, molecular weight, isoelectric point, and instability coefficient of all the Dof proteins in physic nut were predicted using ExPASy Proteomics Server (Available online: http://prosite.expasy. org/) [44]. The orthologous genes of JcDof proteins in *A. thaliana* were predicted by BLASTP.
