Abstract
<italic>F. suspense</italic> is not only an important traditional Chinese medicine and but also an excellent urban greening tree species, thus has important economic and ecologic values. However, the lack of gene resources limits the molecular biology and gene functional studies in <italic>F. suspensa</italic>. In this study, the transcriptome of the mixed samples from root, stem, leaf, flower and fruit of <italic>F. suspensa</italic> was sequenced using the Illumina HiSeq<sup>TM</sup> 2500 sequencing platform. After high through-put sequencing, a total of 23164327 clean reads with 4678791021 bp were obtained. The clean reads were then <italic>de novo</italic> assembled into 45112 unigenes, and 28699 unigenes were annotated by a similarity search against five public databases. Of these annotated unigenes, 473 genes were assigned to second metabolic pathway, including 81 genes associated with phenylalanine and phenylpropanoid metabolism. Further analysis of these 81 genes reveled that there were 4 genes encoding phenylalanine ammonia-lyase, 1 gene encoding cinnamate 4-hydroxylase and 2 genes encoding 4-coumarate: CoA ligase, respectively. These enzymes are involved in the biosynthesis of cinnamic acid derivatives, which are precursors of the mainly pharmaceutically active substances phenylethanoid glycosides and lignan in <italic>F. suspensa</italic>. In addition, we also identified 2 pinoresinol/lariciresinol reductase encoding genes and 1 secoisolariciresinol dehydrogenase encoding gene, which are the key genes in the lignan biosynthesis. Finally, a total of 3199 SSRs were identified from 12721 unigenes longer than 1 kb, and 40 of them were verified. This work not only provides many valuable basal data for gene cloning and molecular biology research, but also lays the foundation for genetic diversity analysis, finger printing construction and molecular marker assisted breeding in <italic>F. suspensa</italic>.
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