Transcriptome analysis of differentially expressed unigenes involved in flavonoid biosynthesis during flower development of Chrysanthemum morifolium ‘Chuju’

Chrysanthemum morifolium is an ornamentally and medicinally important plant species. Up to date, molecular and genetic investigations have largely focused on determination of flowering time in the ornamental species. However, little is known about gene regulatory networks for the biosynthesis of flavonoids in the medicinal species. In the current study, we employed the high-throughput sequencing technology to profile the genome-wide transcriptome of C. morifolium ‘Chuju’, a famous medicinal species in traditional Chinese medicine. A total of 63,854 unigenes with an average length of 741 bp were obtained. Bioinformatic analysis has identified a great number of structural and regulatory unigenes potentially participating in the flavonoid biosynthetic pathway. According to the comparison of digital gene expression, 8,370 (3,026 up-regulated and 5,344 down-regulated), 1,348 (717 up-regulated and 631 down-regulated) and 944 (206 up-regulated and 738 down-regulated) differentially expressed unigenes (DEUs) were detected in the early, middle and mature growth phases, respectively. Among them, many DEUs were implicated in controlling the biosynthesis and composition of flavonoids from the budding to full blooming stages during flower development. Furthermore, the expression patterns of 12 unigenes involved in flavonoid biosynthesis were generally validated by using quantitative real time PCR. These findings could shed light on the molecular basis of flavonoid biosynthesis in C. morifolium ‘Chuju’ and provide a genetic resource for breeding varieties with improved nutritional quality.