title: Transcriptome Analysis of Nine Tissues to Discover Genes Involved in  the Biosynthesis of Active Ingredients in Sophora flavescens.
abstract: Sophora flavescens AITON (kurara) has long been used to treat various diseases. Although several research findings revealed the biosynthetic pathways of its characteristic chemical components as represented by matrine, insufficient analysis of transcriptome data hampered in-depth analysis of the underlying putative genes responsible for the biosynthesis of pharmaceutical chemical components. In this study, more than 200 million fastq format reads were generated by Illumina's next-generation sequencing approach using nine types of tissue from S. flavescens, followed by CLC de novo assembly, ultimately yielding 83,325 contigs in total. By mapping the reads back to the contigs, reads per kilobase of the transcript per million mapped reads values were calculated to demonstrate gene expression levels, and overrepresented gene ontology terms were evaluated using Fisher's exact test. In search of the putative genes relevant to essential metabolic pathways, all 1350 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. By analyzing expression patterns, we proposed some candidate genes involved in the biosynthesis of isoflavonoids and quinolizidine alkaloids. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The preferential expression of the gene for putative lysine/ornithine decarboxylase committed in the initial step of matrine biosynthesis in leaves and stems was confirmed in semi-quantitative polymerase chain reaction (PCR) analysis. The findings in this report may serve as a stepping-stone for further research into this promising medicinal plant.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University; Chuo-ku, Chiba 260–8675, Japan: 2) Pharmacy College, Liaoning University of Traditional Chinese Medicine; DD-Port, Dalian 116600, People’s Republic of China.
authors.forename: Rongchun
authors.initials: R
authors.lastname: Han
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Michimi
authors.initials: M
authors.lastname: Nakamura
authors.forename: Somnuk
authors.initials: S
authors.lastname: Bunsupa
authors.forename: Naoko
authors.initials: N
authors.lastname: Yoshimoto
authors.forename: Hirobumi
authors.initials: H
authors.lastname: Yamamoto
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shibata
authors.forename: Mami
authors.initials: M
authors.lastname: Yamazaki
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
mesh_terms: D000470:Alkaloids / Q000096:biosynthesis*; D020224:Expressed Sequence Tags; D005419:Flavonoids / Q000096:biosynthesis*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D009955:Ornithine Decarboxylase / Q000378:metabolism; D008517:Phytotherapy; D010936:Plant Extracts / Q000096:biosynthesis*; D018515:Plant Leaves / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018547:Plant Stems / Q000378:metabolism; D011807:Quinolizines; D017422:Sequence Analysis, DNA; D029909:Sophora / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome; D000093842:Matrines
chemical_list: D000470:Alkaloids; D005419:Flavonoids; D010936:Plant Extracts; D010940:Plant Proteins; D011807:Quinolizines; D009955:Ornithine Decarboxylase; D000093842:Matrines