Comparative transcriptome analysis and identification of flavonoid biosynthesis related genes from fruits of different Ficus hirta varieties.

Ficus hirta, a well-known medicinal and edible fruit crop widely distributed in the temperate and subtropical areas of China, is rich of flavonoids. However, up to now, the genetic and molecular mechanisms of flavonoid biosynthesis in F. hirta are still unclear. In this study, we assembled the transcriptome of F. hirta using the third-generation sequencing technique single molecule real-time sequencing (SMRT-seq). Then, comparative transcriptome analysis was performed to investigate the fruit gene expression profiling differences among four F. hirta varieties with different lobed leaves (undivided (ud), three-lobed-finger (tf), five-lobed-finger (ff) and seven-lobed-finger (sf)) using RNA-seq. Totally, we obtained 534,375 full-length non-chimeric (FLNC) reads with an average length of 2178 bp by using SMRT-Seq, and 22,782,329, 22,361,639, 21,982,877, and 22,479,690 clean reads for each F. hirta fruit by using RNA-Seq, respectively. Of the assembled 48,399 transcripts, 21,971, 19,183, 21,834, 14,277, 16,255, 16,255 and 21,089 were successfully annotated by NR, SwissProt, KEGG, KOG, Pfam, GO and NT, respectively. And 96 and 21 transcripts were identified to be involved in the phenylpropanoid and flavonoid biosynthesis, respectively. Furthermore, we identified 6, 5, 7, 8, 13 and 14 flavonoid biosynthesis related DEGs in comparison of ud versus tf, ud versus sf, ud versus sf, tf versus ff, tf versus sf and ff versus sf, respectively. And the differential expression of 6 DEGs were confirmed by using quantitative real time PCR. Our study can provide basis for understanding metabolism differences of the bioactive phytochemicals especially flavonoids among different F. hirta varieties. [ABSTRACT FROM AUTHOR]