title: De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens.
abstract: Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant's roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms.
authors.affiliation: College of Resources and Environment, Yuxi Normal University, Yuxi 653100, China. zxd95@126.com.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Plant and Food Research, Mt Albert Research Centre, Private Bag, Auckland 92169, New Zealand. andrew.allan@plantandfood.co.nz.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Allan
authors.affiliation: College of Resources and Environment, Yuxi Normal University, Yuxi 653100, China. licaixia1112@126.com.
authors.forename: Caixia
authors.initials: C
authors.lastname: Li
authors.affiliation: Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming 650223, China. boletus@126.com.
authors.forename: Yuanzhong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: University of Chinese Academy of Sciences, Beijing 100039, China. yaoqiuyang@mail.kib.ac.cn.
authors.forename: Qiuyang
authors.initials: Q
authors.lastname: Yao
mesh_terms: D053898:Biosynthetic Pathways; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D030012:Gentiana / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D057888:Iridoid Glucosides / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010946:Plants, Medicinal / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D013729:Terpenes / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D057888:Iridoid Glucosides; D013729:Terpenes; D014157:Transcription Factors; C012997:gentiopicroside
keywords: Gentiana rigescens; gentiopicroside; regulation; transcriptome