Red flesh color and seedlessness are two important fruit quality traits of Citrus.For flesh color,we have exploited several spontaneous red flesh bud mutants,and global transcriptional analysis on a mutant,using massively parallel signature sequencing (Illumina platform) was applied to decipher the genome-wide gene expression changes,and the results indicated that 3,738 genes show more than two fold expression differences between MT and WT.Meanwhile,comparative proteomic analyses were performed between the mutant and its wild type by using 2DE MALDI-TOF-TOF MS,and a total of 74 differentially expressed proteins were identified.Moreover,to investigate the possible posttranscriptional mechanism,high-throughput pyrosequencing was used to identify and quantitatively profile small RNAs in MT and WT,and comparative profiling revealed that 48 known and 12 novel miRNAs exhibited significant expression differences.All these data provide possible transcriptional and post-transcriptional mechanisms underlying the mutant red-flesh trait formation in sweet orange.