(a–e) Phylogenetic analyses of PHE1-targeted PEGs and their homologs. Each panel represents a distinct target gene and its corresponding homologs in different species. The genes shown on a grey background have homologous RC/Helitron sequences in their promoter region. The arrow indicates the putative insertion of an ancestral RC/Helitron. The identity of the RC/Helitron identified in A. thaliana is indicated. These A. thaliana RC/Helitrons contain a PHE1 DNA-binding motif and are associated with a PHE1 binding site. The inset boxes represent the alignment between the A. thaliana PHE1 DNA-binding motif and similar DNA motifs contained in RC/Helitrons that are present in the promoter regions of orthologous genes. When available, the imprinting status of a given gene is indicated by the presence of ♂ (PEG) or ⚥ (non-imprinted), and reflects the original imprinting analyses done in the source publications (see Materials and methods). The maternal:total read ratio (M/T) for each gene is also indicated. §: potential contamination from maternal tissue. *: accession-biased expression. The scale bars represent the frequency of substitutions per site for the ML tree. The tree is unrooted. Gene identifier nomenclatures: AT, Arabidopsis thaliana; AL, Arabidopsis lyrata; Araha, Arabidopsis halleri; Bostr, Boechera stricta; Carubv, Capsella rubella; Cagra, Capsella grandiflora; Tp, Schrenkiella parvula; SI, Sisymbrium irio; Bol, Brassica oleracea; Brapa, Brassica rapa; Thhalv, Eutrema salsugineum; AA, Aethionema arabicum; THA, Tarenaya hassleriana; Cpa, Carica papaya; TCA, Theobroma cacao; Gorai, Gossypium raimondii; RCO, Ricinus communis; FVE, Fragaria vesca; and GSVIVG, Vitis vinifera.