RNA-Seq Analysis of Coscinium fenestratum (Gaertn.) Colebr a Critically Endangered Medicinal Plant from Western Ghats of India

Coscinium fenestratum (Gaertn.) Colebr. is a seed propagated dioecious woody liana belonging to the tribe Coscinieae, the smallest tribe of family Menispermaceae. 1997 IUCN Red list of threatened plants recorded the status of C. fenestratum as endangered in India, vulnerable in Vietnam, rare in Singapore and indeterminate in Sri Lanka. Herbal remedies are increasingly being recognized in recent years as alternative medicine for a number of diseases including diabetes mellitus. This species is of particular interest due to its medicinal properties and presence of Benzylisoquinoline alkaloids (BIAs) particularly Berberine which is known to have several biological activities. The stem of the plant has anti-diabetic, anti-microbial, anti-inflammatory, anti-oxidants properties used for curing several diseases. Berberine, a secondary metabolite isolated from the stems of this plant has been shown to have significant anti-diabetic properties, in addition to antimicrobial and antioxidant effects. We sequenced the stem transcriptome of C.fenestratum using Illumina HiSeq 2000 paired-end sequencing followed by de novo transcriptome assembly. After de novo assembly and quantitative assessment, 70,919 unigenes were finally generated with an average length of 631 bp. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and benzoisoquinoline alkaloid biosynthesis pathways. We were successful in annotating the complete set of Berberine Biosynthesis pathway genes. Our data not only provides molecular signatures for several alkaloid pathways but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. fenestratum. Understanding the role in the BIAs biosynthetic genes will provide the parts required to for emerging synthetic biology platforms which exploits microbes as an alternative to plants as a commercial source for production of valuable BIAs, which will minimize the dependence on the natural resource thereby conserving plants at the verge of extinction.  This work sets the stage for multi-faceted future improvement of the C. fenestratum plant, through discovery of new genes, marker-assisted breeding or genetic engineering for production of important plant secondary metabolites, on this species as well as for other important medicinal plants which are at the verge of extinction.