*4.4. Analyses of Intron–Exon Structure, Genome Distribution, and Gene Duplications*

Genomic sequences (apple v1.0), gene distributions on chromosomes, and genome locations of SAPs in apple and 31 other species were downloaded from Plaza 3.0 (Supplementary Sequence A1) [48]. The structural features of these *MdSAP* genes, including exons/introns, numbers, and locations, were obtained and presented by using the gene structure display server (GSDS) web-based bioinformatics tool (http://gsds.cbi.pku.edu.cn/) [49]. The chromosomal positions of all of the *MdSAP* genes were

located via MapInspect (www.plantbreeding.wur.nl/UK/software\_mapinspect.html) [50]. Segmental and tandem-duplication events were investigated according to the method of Tian et al. [31].
