De novo Transcriptome and tissue specific expression analysis of gene associated with biosynthesis of medicinally active metabolites in a high valued medicinal plant Operculina turpethum (L.)

Abstract

Operculina turpethum (L.) Silva Manso (Nisoth), an important medicinal plant whose root and stem tissues are found to be key ingredient in more than 135 herbal formulation in both Unani and Ayurvedic medicine system and is used for the treatment of various health disorders. It has a very high demand in the Indian Pharmaceutical industry with an annual average consumption of about 660 metric tonne (dry weight). The plant because of its wide usability is also exported to countries like Sri Lanka, Singapore, Netherlands, Japan, United States, etc. leading to a total export value of approximately 2.4 million USD. Terpenoids, steroid glycosides, resin glycosides, dammarane type triterpenoid saponins, flavonoids, coumarins are the major bioactive principles present in O. turpethum. However, overexploitation of root/root bark over the other part of the plant has caused depletion of its germplasm resources from the wild while bringing it to Near Threatened category which subsequently lead to unavailability of the requisite plant material followed by adulteration. Additionally, the limited genomics and transcriptomic resource is a major hindrance in the genetic and molecular research including elucidation of biosynthetic pathway, identification of enhanced traits and proper authentication and genetic diversity study of the plant. Hence, de novo transcriptome sequencing of root and stem tissues of O. turpethum was performed using Illumina HiSeq platform which generated a total of 64259 unigenes and 20870 CDS (coding sequence) with a mean length of 449bp and 571bp respectively. Further, 20218 and 16458 unigenes showed significant similarity with the identified proteins of NR(non-redundant) and Uniprot database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. Moreover, transcription factors, SSRs (Simple sequence repeats) and SNPs (single nucleotide polymorphism) were also identified in this study. Apparently, the present investigation reported the first ever transcriptome analysis of the root and stem tissues of the non-model plant O. turpethum of family Convolvulaceae, which will provide a baseline for further molecular research.

Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta

“…(Kanehisa and Sato 2019). Similar studies were reported in Hevea brasiliensis (Li et al 2012), Ipomoea batatas (Wang et al 2010;Xie et al 2012), Solanum trilobatum (Lateef et al 2018), Gasterophilus nasalis (Zang et al 2021), Operculina turpethum (Biswal et al 2021) and Juglans mandshurica (Yan et al 2021). Importantly, the KO was also annotated through GAEV; hence, pathways with their number of associated genes were also obtained (Iacobas et al 2019;Emami-Khoyi et al 2020;Nand et al 2020;Shah et al 2021).…”