title: Transcriptome sequencing of Codonopsis pilosula and identification of candidate genes involved in polysaccharide biosynthesis.
abstract: BACKGROUND
  Codonopsis pilosula (Franch.) Nannf. is one of the most widely used medicinal plants. Although chemical and pharmacological studies have shown that codonopsis polysaccharides (CPPs) are bioactive compounds and that their composition is variable, their biosynthetic pathways remain largely unknown. Next-generation sequencing is an efficient and high-throughput technique that allows the identification of candidate genes involved in secondary metabolism.
  
  
  RESULTS
  To identify the components involved in CPP biosynthesis, a transcriptome library, prepared using root and other tissues, was assembled with the help of Illumina sequencing. A total of 9.2 Gb of clean nucleotides was obtained comprising 91,175,044 clean reads, 102,125 contigs, and 45,511 unigenes. After aligning the sequences to the public protein databases, 76.1% of the unigenes were annotated. Among these annotated unigenes, 26,189 were assigned to Gene Ontology categories, 11,415 to Clusters of Orthologous Groups, and 18,848 to Kyoto Encyclopedia of Genes and Genomes pathways. Analysis of abundance of transcripts in the library showed that genes, including those encoding metallothionein, aquaporin, and cysteine protease that are related to stress responses, were in the top list. Among genes involved in the biosynthesis of CPP, those responsible for the synthesis of UDP-L-arabinose and UDP-xylose were highly expressed.
  
  
  CONCLUSIONS
  To our knowledge, this is the first study to provide a public transcriptome dataset prepared from C. pilosula and an outline of the biosynthetic pathway of polysaccharides in a medicinal plant. Identified candidate genes involved in CPP biosynthesis provide understanding of the biosynthesis and regulation of CPP at the molecular level.
authors.affiliation: College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China.
authors.forename: Jian Ping
authors.initials: JP
authors.lastname: Gao
authors.affiliation: College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.affiliation: College of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, China.
authors.forename: Ling Ya
authors.initials: LY
authors.lastname: Cao
authors.affiliation: College of Chemistry & Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China.
authors.forename: Hai Feng
authors.initials: HF
authors.lastname: Sun
mesh_terms: D001483:Base Sequence; D029745:Codonopsis / Q000235:genetics*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D011134:Polysaccharides / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome
chemical_list: D011134:Polysaccharides