Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

Kok Keong Loke, Reyhaneh Rahnamaie-Tajadod, Chean Chean Yeoh, Hoe Han Goh, Zeti Azura Mohamed Hussein, Zamri Zainal, Ismanizan Ismail, Normah Mohd. Noor

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background: Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have 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 from Polygonum minus root 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%) of Polygonum minus transcripts, largely from Arabidopsis 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. Discussion: 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 of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/ dataset/transcriptome.

Original languageEnglish
Article numbere2938
JournalPeerJ
Volume2017
Issue number2
DOIs
Publication statusPublished - 2017

Fingerprint

Polygonum
Biosynthesis
phenylpropanoids
Gene Expression Profiling
Metabolites
Metabolic Networks and Pathways
transcriptomics
Transcriptome
Flavonoids
transcriptome
biochemical pathways
flavonoids
Genes
Polygonaceae
secondary metabolites
Tissue
Fragrances
biosynthesis
genes
Expressed Sequence Tags

Keywords

  • 454 sequencing
  • De novo assembly
  • Hybrid assembly
  • Illumina sequencing
  • Persicaria minor
  • RNA-seq

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids. / Loke, Kok Keong; Rahnamaie-Tajadod, Reyhaneh; Yeoh, Chean Chean; Goh, Hoe Han; Mohamed Hussein, Zeti Azura; Zainal, Zamri; Ismail, Ismanizan; Mohd. Noor, Normah.

In: PeerJ, Vol. 2017, No. 2, e2938, 2017.

Research output: Contribution to journalArticle

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AU - Rahnamaie-Tajadod, Reyhaneh

AU - Yeoh, Chean Chean

AU - Goh, Hoe Han

AU - Mohamed Hussein, Zeti Azura

AU - Zainal, Zamri

AU - Ismail, Ismanizan

AU - Mohd. Noor, Normah

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