title: De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products.
abstract: Study on transcriptome, the entire pool of transcripts in an organism or single cells at certain physiological or pathological stage, is indispensable in unraveling the connection and regulation between DNA and protein. Before the advent of deep sequencing, microarray was the main approach to handle transcripts. Despite obvious shortcomings, including limited dynamic range and difficulties to compare the results from distinct experiments, microarray was widely applied. During the past decade, next-generation sequencing (NGS) has revolutionized our understanding of genomics in a fast, high-throughput, cost-effective, and tractable manner. By adopting NGS, efficiency and fruitful outcomes concerning the efforts to elucidate genes responsible for producing active compounds in medicinal plants were profoundly enhanced. The whole process involves steps, from the plant material sampling, to cDNA library preparation, to deep sequencing, and then bioinformatics takes over to assemble enormous-yet fragmentary-data from which to comb and extract information. The unprecedentedly rapid development of such technologies provides so many choices to facilitate the task, which can cause confusion when choosing the suitable methodology for specific purposes. Here, we review the general approaches for deep transcriptome analysis and then focus on their application in discovering biosynthetic pathways of medicinal plants that produce important secondary metabolites.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
authors.forename: R
authors.initials: R
authors.lastname: Han
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
authors.forename: A
authors.initials: A
authors.lastname: Rai
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Medical Mycology Research Center, Chiba University, Chiba, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Yamazaki
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Japan. Electronic address: ksaito@faculty.chiba-u.jp.
authors.forename: K
authors.initials: K
authors.lastname: Saito
mesh_terms: D001688:Biological Products / Q000378:metabolism*; D053898:Biosynthetic Pathways; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010946:Plants, Medicinal / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics; D064210:Secondary Metabolism; D059467:Transcriptome
chemical_list: D001688:Biological Products; D018749:RNA, Plant
keywords: Biosynthetic pathway; Deep transcriptome; Gene discovery; Medicinal plant; RNA-Seq