Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4′-tetrahydroxy stilbene-2-O-β-d-glucoside

• 65,653 unigenes in Fallopia multiflora were obtained by RNA-seq.
• Variations in gene expression were identified from two F. multiflora roots.
• THSG may be synthesized from tyrosine initiation.

The compound 2,3,5,4′-tetrahydroxy stilbene-2-O-ß-d-glucoside (THSG) synthesized by Fallopia multiflora (F. multiflora) exhibits pharmacological potency. However, the mechanistic details of its biosynthesis pathway are still vague. To clear this ambiguity, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of F. multiflora using the Illumina RNA-seq system. RNA-seq generated approximately 70 million high-quality reads that were assembled into 65,653 unigenes (mean length = 750 bp), including 26,670 clusters and 38,983 singletons. A total of 48,173 (73.4%) unigenes were annotated using public protein databases with a cut-off e-value above 10− 5. Furthermore, we investigated the transcriptome difference of four different F. multiflora tissues using DGE profiling. Variations in gene expression were identified based on comparisons of transcriptomes from various parts of a high-level THSG- and a low-level THSG-producing F. multiflora plant. Clusters with similar differential expression patterns and enriched metabolic pathways with regard to the differentially expressed genes putatively involved in THSG biosynthesis were revealed for the first time. Our data provides the most comprehensive sequence resource regarding F. multiflora so far. Taken together, the results of this study considerably extend the knowledge on THSG production.