Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq

摘要

Hypericum perforatum is a traditional medicinal plant used for various purposes since ancient times because of the valuable secondary metabolites. The genomic information for H. perforatum is limited and the regulatory networks of secondary metabolism are still unknown. The naphthodianthrone hypericin is the metabolite of our main interest. It is a red-colored photodynamic pigment localized in dark glands of some Hypericum species. High-throughput sequencing technology, especially RNA-Seq, followed by de novo assembly and analysis of differential gene expression provides an important tool for functional genomics of non-model organisms. It represents an opportunity of insight into dynamic biological processes including those of secondary metabolism. Transcriptome analysis followed by the analysis of differential gene expression of H. perforatum leaf tissues containing and lacking dark glands was performed to identify the genes involved in hypericin biosynthesis and to profile expression patterns in greater detail. A total of 18.53 G of cleaned read nucleotides were generated and assembled into 139,959 contigs with N50 of 1801 bp. Among them, 66,817 (47.74 %) contigs were annotated. Differentially expressed genes were discovered by comparison of dark glands with adjacent leaf tissue and contrasting inner part leaf tissue without dark glands. A total of 799 upregulated genes were found in the tissues containing dark glands and 263 enzymes were identified, including candidate genes of hypericin biosynthesis, especially the genes coding for polyketide synthases and those involved in defense reactions. This study determined candidate genes involved in hypericin biosynthesis providing a valuable source for perspective metabolic engineering of bioactive substances.