Comparative transcriptome profiling unveils the potential key genes involved in peel coloration between Ziziphus mauritiana Lam. and Z. jujuba Mill

Ber (Ziziphus mauritiana Lam.) is one of the important tropical and subtropical fruit trees of the genus Ziziphus Mill. Most cultivars of Ber keep green throughout fruit development while its close relative Chinese jujube (Z. jujuba Mill.) changes the color from green to red in all cultivars. However, the lack of transcriptomic and genomic information limits our insights into the molecular mechanisms underpinning fruit coloration in Ber. Here, high-throughput RNA sequencing (RNA-Seq) was used for the first time to de novo assemble and characterize the transcriptome of Ber fruit. Over 20 million clean reads were produced, and 62,029 unigenes with an average length of 1078.76 bp were assembled. The differentially regulated genes that are responsive to fruit color were also studied in Ber. Eight structural genes, ZmC4H1, ZmBIA1, ZmLDOX, and ZmUGT (UTG6, UFGT13 UFGT14, UFGT15, and UFGT16), were found to be significantly differentially expressed and downregulated in Ber fruit peel, indicating that these genes may be involved in no color formation in the fruit peel of Ber. Furthermore, transcription factors such as bHLH and ZmMYB (MYB13, 14 15, and 16) were found to be downregulated at five developmental stages of Ber fruit, suggesting an important interconnection with flavonoids like anthocyanin biosynthesis-related genes. The expression of these selected genes was also checked at all fruit developmental stages in the Chinese jujube transcriptome. All the selected genes were significantly up-regulated in the fruit developmental stages of Jujube. The expression pattern of these selected genes encoding flavonoid or anthocyanin biosynthetic enzymes and transcription factors in the Ber and Jujube fruit peels were confirmed using quantitative real-time PCR. This study provided insights into the diversity of fruit coloration in Ziziphus Mill. and will serve as a new starting point for further functional investigation of these genes.