Transcriptome and genome re-sequencing analysis reveals differential expression patterns and sequence variation in pericarp wax metabolism-related genes in Ziziphus jujuba (Chinese jujube)

•A combination of transcriptome and genome re-sequencing was used to explore one of the main factors leading to fruit cracking in jujube, namely the difference in wax metabolism between jujube cultivars (‘Linhuang No. 1’ and ‘Muzao’) with different cracking sensitivity.•The wax form of the ‘Muzao’ fruit was fissured during the mature period. The fatty acid content of ‘Linhuang No. 1’ was always significantly greater than that of ‘Muzao’ under control (CK) or hormone treatments. The proportion of total fatty acids with fewer than 16 C atoms in ‘Linhuang No. 1’ was less than in ‘Muzao’. All of these are due to the loss of 107 bases in the promoter region of the LOC107415896 in ‘Muzao’, which encodes the protein of biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (BCCP2).•This research could be helpful in explaining divergence/similarity of wax metabolism-related genes between the two cultivars and their possible role in fruit cracking. The fruit pericarp wax of jujube accessions with different cracking resistance show differences in morphology and wax chemical content. In this study, transcriptome and genome re-sequencing were used to analyze the differences in wax metabolism between jujube cultivars with different cracking resistance characteristics. The results showed that 431 differentially expressed genes were identified through transcriptome screening between the cracking-resistant cultivar ‘Linhuang No. 1’ and the cracking-susceptible cultivar ‘Muzao’ during the mature stage of fruit development. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis annotated three wax metabolism pathways (involving eight wax metabolism-related genes). Information on gene sequence variation in the eight genes was obtained from genome resequencing, with sequence variation between the two cultivars found in the promoter region of the LOC107415896 gene, which encodes the biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (BCCP2) protein, where 107 bases were inserted in ‘Linhuang No.1’. As a result, the fatty acid concentration in the wax of ‘Muzao’ was lower than that of ‘Linhuang No. 1’, with the proportion of fatty acids with fewer than 16 C atoms in ‘Muzao’ accounting for a greater proportion of the total fatty acids. This indicated that the expression of the ‘Muzao’ LOC107415896 gene was affected. Our research has laid the foundation for further analysis of the function of jujube wax metabolism in the cra