title: Transcriptome analysis ofPolygonum minusreveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids.
abstract: BACKGROUND
  Polygonum minusis an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance ofPolygonum minushave been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production.
  
  
  METHODS
  In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads fromPolygonum minusroot and leaf tissues, respectively, to generate a combined transcriptome library as a reference.
  
  
  RESULTS
  A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) ofPolygonum minustranscripts, largely fromArabidopsis thaliana(58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites.
  
  
  CONCLUSIONS
  This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly ofPolygonum minuscan be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Malaysia.
authors.forename: Kok-Keong
authors.initials: KK
authors.lastname: Loke
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Malaysia.
authors.forename: Reyhaneh
authors.initials: R
authors.lastname: Rahnamaie-Tajadod
authors.affiliation: School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia , Bangi , Malaysia.
authors.forename: Chean-Chean
authors.initials: CC
authors.lastname: Yeoh
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Malaysia.
authors.forename: Hoe-Han
authors.identifier: 0000-0002-8508-9977
authors.initials: HH
authors.lastname: Goh
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia; School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia.
authors.forename: Zeti-Azura
authors.initials: ZA
authors.lastname: Mohamed-Hussein
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia; School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia.
authors.forename: Zamri
authors.initials: Z
authors.lastname: Zainal
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia; School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia.
authors.forename: Ismanizan
authors.initials: I
authors.lastname: Ismail
authors.affiliation: Institute of Systems Biology, Universiti Kebangsaan Malaysia , Bangi , Malaysia.
authors.forename: Normah
authors.initials: N
authors.lastname: Mohd Noor
keywords: 454 sequencing; De novo assembly; Hybrid assembly; Illumina sequencing; Persicaria minor; RNA-seq