title: Transcriptomic analysis of Pseudostellariae Radix from different fields using RNA-seq.
abstract: Pseudostellariae Radix is an important traditional Chinese medicine (TCM), which is consumed commonly for its positive health effects. However, a lack of transcriptomic and genomic information hinders research on Pseudostellariae Radix. Here, high-throughput RNA sequencing (RNA-seq) was employed for the de novo assembly to analyze the transcriptome in Pseudostellariae Radix, finding significantly differentially expressed genes in this TCM from different fields based on RNA-seq and bioinformatic analysis. A total of 146,408,539 paired-end reads were generated and assembled into 89,857 unigenes with an average length of 862bp. All of the assembly unigenes were annotated by running BLASTx and BLASTn similarity searches on the Non-redundant nucleotide database (NT), the Non-redundant protein database (NR), Swiss-Prot, Cluster of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Interpro. On the basis of bioinformatic analysis and the expression profiles for Pseudostellariae Radix, 29 significantly differentially expressed genes were identified, which provides the basic information for exploring the molecular mechanisms that determine the quality of Pseudostellariae Radix from different fields. The expression levels of 29 genes were validated by real-time quantitative PCR (RT-qPCR). This is the first study to sample Pseudostellariae Radix, which provides an invaluable resource for understanding the genome of this herb.
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Yujiao
authors.initials: Y
authors.lastname: Hua
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Shengnan
authors.initials: S
authors.lastname: Wang
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Zixiu
authors.initials: Z
authors.lastname: Liu
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China. Electronic address: liuxunh1959@sohu.com.
authors.forename: Xunhong
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Lisi
authors.initials: L
authors.lastname: Zou
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Gu
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Yiyuan
authors.initials: Y
authors.lastname: Luo
authors.affiliation: School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
authors.forename: Juanxiu
authors.initials: J
authors.lastname: Liu
mesh_terms: D029748:Caryophyllaceae / Q000235:genetics* / Q000378:metabolism; D002681:China; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
keywords: Cultivated fields; Pseudostellariae Radix; RNA-seq; Traditional field; Transcriptome