Fig. 5

Expression levels of genes in regions that overlapped between SVs and presence/absence variations (PAVs) were compared between ‘Bartlett’ and ‘Dangshansuli’ pear samples to identify genes potentially associated with important agronomic traits. A, B Venn diagram showing SVs identified using three different SV detection programs on PB-CLR and ONT sequencing data, respectively. C, D KEGG pathway enrichment analysis of differentially expressed genes (DEGs) with SVs located in the promoter region. DEGs are shown as down-regulated (C) or up-regulated (D) in ‘Dangshansuli’ compared to ‘Bartlett’. E–H FPKM values of four candidate genes related to sugar, lignin, and fatty acid biosynthesis pathways