*2.5. Genome Distribution of Apple SAP Genes*

We determined the genomic locations of these apple SAP genes based on their mapping coordinates. In all, 28 of the 30 *MdSAP* genes were assigned to chromosomes 1–4, 6–9, 11, 12, 14, and 17 (Table 1; Figure 5). However, we could not conclusively map two genes (*MdSAP29* and *MdSAP30*) to any chromosome. The genes were unevenly distributed among the 12 chromosomes, with Chromosome 2 containing the most (eight genes), followed by Chromosome 7 (five genes), and one each for chromosomes 1, 3, 6, 12, and 14.

The apple gene family appears to have expanded during the process of genome evolution [26]. To uncover the mechanism underlying this expansion, we investigated gene duplication events, including tandem and segmental duplications, and found that many *MdSAP* genes (19/30, or 63.33%) were present in two or more copies (Figure 5). In all, 17 had undergone tandem duplication, while two were subjected to segment duplication. Those segment duplications produced many homologs of SAP genes on different chromosomes, while tandem duplications produced SAP gene clusters or hotspots (blue and red font in Figure 5). A relatively recent genome-wide duplication is that in the Pyreae tribe, which was thought to result in the transition of nine ancestral chromosomes to 17 chromosomes [26]. We noted here that multiple gene pairs were each linked to at least six potential chromosomal segmental duplications (Figure 5, pairs of bars in grey areas), e.g., large sections of chromosomes 9 and 17, 3 and 11, and 7 and 2.

**Figure 5.** Chromosomal locations of 28 apple SAP genes. Scale is in megabases (Mb). Red font, tandem duplication; blue font, segmental duplication; grey area, genome-wide duplications.
