title: De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome.
abstract: Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P. heterophylla. We obtained 616,413,316 clean reads that we assembled into 127, 334 unique sequences with an N50 length of 951 bp. Among these unigenes, 53,184 unigenes (41.76%) were annotated in a public database and 39, 795 unigenes were assigned to 356 KEGG pathways; 23,714 unigenes (8.82%) had high homology with the genes from Beta vulgaris. We discovered 32, 095 DEGs in different tissues and performed GO and KEGG enrichment analysis. The most enriched KEGG pathway of secondary metabolism showed up-regulated expression in tuberous roots as compared with the ground parts of P. heterophylla. Moreover, we identified 72 candidate genes involved in triterpenoids saponins biosynthesis in P. heterophylla. The expression profiles of 11 candidate unigenes were analyzed by quantitative real-time PCR (RT-qPCR). Our study established a global transcriptome database of P. heterophylla for gene identification and regulation. We also identified the candidate unigenes involved in triterpenoids saponins biosynthesis. Our results provide an invaluable resource for the secondary metabolites and physiological processes in different tissues of P. heterophylla.
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhen
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Dengkai
authors.initials: D
authors.lastname: Long
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Ding
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Anhui
authors.initials: A
authors.lastname: Gong
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Chenghong
authors.initials: C
authors.lastname: Xiao
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Weike
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Liu
authors.affiliation: Guiyang University of Chinese Medicine, Guiyang 550025, China.|National Engineering Research Center of Miao's Medicines, Guiyang 550025, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Luqi
authors.initials: L
authors.lastname: Huang
mesh_terms: D029748:Caryophyllaceae / Q000235:genetics* / Q000378:metabolism; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant