title: High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome.
abstract: Perilla frutescens var. crispa (Labiatae) has two chemo-varietal forms, i.e. red and green forms of perilla, that differ in the production of anthocyanins. To facilitate molecular biological and biochemical studies in perilla-specialized metabolism we used Illumina RNA-sequencing technology in our comprehensive comparison of the transcriptome map of the leaves of red and green forms of perilla. Sequencing generated over 1.2 billion short reads with an average length of 101 nt. De novo transcriptome assembly yielded 47,788 and 47,840 unigenes in the red and green forms of perilla plants, respectively. Comparison of the assembled unigenes and existing perilla cDNA sequences showed highly reliable alignment. All unigenes were annotated with gene ontology (GO) and Enzyme Commission numbers and entered into the Kyoto Encyclopedia of Genes and Genomes. We identified 68 differentially expressed genes (DEGs) in red and green forms of perilla. GO enrichment analysis of the DEGs showed that genes involved in the anthocyanin metabolic process were enriched. Differential expression analysis revealed that the transcript level of anthocyanin biosynthetic unigenes encoding flavonoid 3'-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase was significantly higher in red perilla, while the transcript level of unigenes encoding limonene synthase was significantly higher in green perilla. Our data serve as a basis for future research on perilla bio-engineering and provide a shortcut for the characterization of new functional genes in P. frutescens.
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Fukushima
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263-8522, Japan.
authors.forename: Michimi
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263-8522, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba, 263-8522, Japan.
authors.forename: Mami
authors.initials: M
authors.lastname: Yamazaki
mesh_terms: D000872:Anthocyanins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D031344:Perilla frutescens / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D000872:Anthocyanins