Abstract
BackgroundPolygonum 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.MethodsIn 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.ResultsA 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.DiscussionThis 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.
Highlights
Secondary metabolites are organic compounds that are non-vital but indirectly influence plant survival, development and growth
The abundance of secondary metabolites in Polygonum minus has led to the establishment of hairy root system for the production of plant secondary metabolites (Ashraf et al, 2014). b-caryophyllene was found to be the main sesquiterpenes secreted into the hairy root culture media
A cross comparison of 3,538 Polygonum minus expressed sequences tag (EST) from a previous study against the combined assembly shows 100% reciprocal hits (Table S2) which supports a comprehensive coverage of the combined assembly
Summary
Secondary metabolites are organic compounds that are non-vital but indirectly influence plant survival, development and growth. Plant secondary metabolites are important natural sources for the development of medicines and natural products. B-caryophyllene was found to be the main sesquiterpenes secreted into the hairy root culture media These studies showed the potential of developing Polygonum minus as a resource to produce natural products. There are only a few transcriptome sequences available for species from this important family of medicinal plants. 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. 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
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