title: High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites.
abstract: Here, we report potential transcripts involved in the biosynthesis of therapeutic metabolites in Swertia japonica , the first report of transcriptome assembly, and characterization of the medicinal plant from Swertia genus. Swertia genus, representing over 170 plant species including herbs such as S. chirata, S. hookeri, S. longifolia, S. japonica, among others, have been used as the traditional medicine in China, India, Korea, and Japan for thousands of years. Due to the lack of genomic and transcriptomic resources, little is known about the molecular basis involved in the biosynthesis of characteristic key bioactive metabolites. Here, we performed deep-transcriptome sequencing for the aerial tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 bps. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding 81,729 unigenes having an average length of 884 bps and N50 value of 1452 bps, of which 46,963 unigenes were annotated based on the sequence similarity against NCBI-nr protein database. Annotation of transcriptome assembly resulted in the identification of putative genes encoding all enzymes from the key therapeutic metabolite biosynthesis pathways. Transcript abundance analysis, gene ontology enrichment analysis, and KEGG pathway enrichment analysis revealed metabolic processes being up-regulated in the aerial tissues with respect to the roots of S. japonica. We also identified 37 unigenes as potential candidates involved in the glycosylation of bioactive metabolites. Being the first report of transcriptome assembly and annotation for any of the Swertia species, this study will be a valuable resource for future investigations on the biosynthetic pathways of therapeutic metabolites and their regulations.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan. amit.rai@chiba-u.jp.
authors.forename: Amit
authors.identifier: http://orcid.org/0000-0002-5715-8541
authors.initials: A
authors.lastname: Rai
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan.
authors.forename: Michimi
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Medical Mycology Research Center, Chiba University, Chiba, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Department of Research and Development, Kazusa DNA Research Institute, Chiba, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan. mamiy@faculty.chiba-u.jp.
authors.forename: Mami
authors.initials: M
authors.lastname: Yamazaki
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D005964:Glucosyltransferases / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D057888:Iridoid Glucosides / Q000737:chemistry / Q000378:metabolism; D039823:Iridoids / Q000737:chemistry / Q000378:metabolism; D055442:Metabolome / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D018517:Plant Roots / Q000235:genetics; D011753:Pyrones / Q000737:chemistry / Q000378:metabolism; D029967:Swertia / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics
chemical_list: D057888:Iridoid Glucosides; D039823:Iridoids; D011753:Pyrones; C013270:swertiamarin; C102609:amarogentin; D005964:Glucosyltransferases
keywords: MEP biosynthesis pathways; S. japonica transcriptome assembly; Secoiridoid metabolic pathways; Swertia genus; Swertiamarin