*2.4. Phylogenetic Analysis of SAP Proteins*

To examine the evolutionary relationships among plant SAP proteins, we used MEGA 6 and constructed unrooted phylogenetic trees from full-length protein sequences encoded by 453 SAP genes in 32 species (Supplementary File B1). Two major groups were revealed: I, containing an A20 domain and an AN1 domain; and II, containing two AN1 domains. Members in Group I were further classified into four subgroups (Ia-Id), while Group II members were assigned to two subgroups: IIa, containing two AN1 domains and one or two C2H2 domain(s); and IIb, containing only two AN1 domains. Among these 30 *MdSAP* proteins, 25 (*MdSAP1*-*MdSAP20*, *MdSAP23*, *MdSAP24*, *MdSAP26*, *MdSAP29*, and *MdSAP30*) could be unambiguously classified as Group I, while four (*MdSAP21*, *MdSAP25*, *MdSAP27*, and *MdSAP28*) were assigned to Group II based on their relationship with the other SAP proteins (Figure 4 and Supplementary File B2). Further analysis revealed that the 25 Group-I apple proteins belonged to subgroups Ia (seven genes), Ib (five), Ic (five), and Id (eight). Subgroup IIa contained *MdSAP25*, while IIb contained *MdSAP21*, *MdSAP27*, and *MdSAP28*.

**Figure 4.** Phylogenetic analysis of 453 SAP proteins in 32 species. Unrooted NJ tree was constructed with MEGA 6 software, using full-length amino acid sequences. Tree comprises six subgroups (Ia–Id; IIa and IIb).
