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

PeerJ

article

Kok-Keong Loke¹  Reyhaneh Rahnamaie-Tajadod¹  Chean-Chean Yeoh²  Hoe-Han Goh¹  Zeti-Azura Mohamed-Hussein¹  Zamri Zainal¹  Ismanizan Ismail¹  Normah Mohd Noor¹ 

[1] Institute of Systems Biology, Universiti Kebangsaan Malaysia;School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia

关键词: De novo assembly;    Hybrid assembly;    Illumina sequencing;    RNA-seq;    Persicaria minor;    454 sequencing;   

DOI  :  10.7717/peerj.2938

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY