*4.2. Sequence Alignments and Phylogenetic Analysis*

We performed multiple sequence alignments of 30 *MdSAP* protein sequences, using DNAMAN 6.0.3.99 with its default parameters [45]. A phylogenetic tree for the SAP gene family was constructed with MEGA 6.0 software (www.megasoftware.net) and the neighbor-joining (NJ) method, together with the full-length amino acid sequences of 453 SAPs from 32 plant species, including apple (Supplementary Sequence A2). Related sequences were downloaded from the resource Plaza 3.0 (http://bioinformatics. psb.ugent.be/plaza/). We used the following parameters in the NJ method: bootstrap (1000 replicates), complete deletion, and amino: *p*-distance [34].
