De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

Abstract

Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.

Figure 1

Taxonomic distribution of Gymnema sylvestre transcripts across plant nr database.

Figure 2

Top 20 GO enriched terms of transcripts in biological processes, cellular components and molecular function.

Figure 3

KEGG analysis showing number of transcripts mapped to enzymes involved in terpenoid pathways.

Figure 4

Transcripts mapped on the Terpenoid Biosynthetic pathway (Enzymes highlighted in one colour code for one enzyme. Green colour depicts different enzyme code). KEGG pathway map 00900 is mined here from http://www.kegg.jp/kegg/kegg1.html. The KEGG database has been reported previously^–.

Figure 5

Transcripts mapped on ubiquinone and other terpenoid-quinone biosynthesis (Enzymes highlighted in one colour code for one enzyme. Green colour depicts different enzyme code). KEGG pathway map 00130 is mined here from http://www.kegg.jp/kegg/kegg1.html. The KEGG database has been reported previously^–.

Figure 6

Transcripts mapped on biosynthesis of sesquiterpenoid and triterpenoid biosynthesis pathway (Enzymes highlighted in one colour code for one enzyme. Green colour depicts different enzyme code). KEGG pathway map 00909 is mined here from http://www.kegg.jp/kegg/kegg1.html. The KEGG database has been reported previously^–.

Figure 7

Transcripts mapped on the flavonoid biosynthetic pathway (Enzymes highlighted in one colour code for one enzyme. Green colour depicts different enzyme code). Green colour depicts different enzyme code). KEGG pathway map 00941 is mined here from http://www.kegg.jp/kegg/kegg1.html. The KEGG database has been reported previously^–.

Figure 8

Transcription factor families detected from Gymnema sylvestre leaf transcriptome.