Transcriptome Analysis of Jujube Cultivars

Phloem, mature leaves, flowers, and fruits at different stages (expanding fruit, half-red, and full-red) of the ‘Junzao’ cultivar and the wild jujube ‘Qingjiansuanzao’ (8 years old) were collected in 2013 and 2014, respectively. All the samples were immediately frozen in liquid nitrogen. Total RNAs were isolated using a modified CTAB method and then treated with RNase-free DNase I (Promega, USA). First-strand cDNAs were synthesized using a Clontech kit. RNA-Seq libraries were constructed using the NEB Next UltraTM RNA Library Prep Kit (NEB, USA) and sequenced on a HiSeq 2000/2500 system. RNA-Seq reads were mapped to the ‘Junzao’ genome using TopHat [38 (link)]. The total numbers of aligned reads (read counts) for each gene were normalized to the reads per kilobase exon model per million mapped reads (RPKM) [66 (link)]. DESeq [67 (link)] was used to identify differentially expressed genes.