Abstract
Holy basil (Ocimum sanctum L.) and sweet basil (Ocimum basilicum L.) are the most commonly grown basil species in India for essential oil production and biosynthesis of potentially volatile and non-volatile phytomolecules with commercial significance. The aroma, flavor and pharmaceutical value of Ocimum species is a significance of its essential oil, which contains most of the monoterpenes and sesquiterpenes. A large number of plants have been studied for characterization and identification of terpene synthase genes, involved in terpenoids biosynthesis. The goal of this study is to discover and identify the putative functional terpene synthase genes in O. sanctum. HMMER search was performed by using a set of 13 well sequenced and annotated plant genomes including the newly sequenced genome of O. sanctum with Pfam-A database locally, using HMMER 3.0 hmmsearch for the two Pfam domains (PF01397 and PF03936). Using this search method 81 putative terpene synthases genes (OsaTPS) were identified in O. sanctum; the study further reveals 47 OsaTPS were putatively functional genes, 19 partial OsaTPS, and 15 OsaTPS as probably pseudogenes. All these identified OsaTPS genes were compared with other plant species, and phylogenetic analysis reveals the subfamily classification of OsaTPS in TPS-a, -b, -c, -e, -f and TPS-g subfamilies clusters. This genome-wide identification of OsaTPS genes, their phylogenetic analysis and secondary metabolite pathway mapping predictions together provide a comprehensive understanding of the TPS gene family in Ocimum sanctum and offer opportunities for the characterization and functional validation of numbers of terpene synthase genes.
Highlights
The terpenes are a large class of plant specialized secondary metabolites, which derived from 5 carbon (C5) isoprenoid unit; these precursors are produced by two biosynthetic pathways, the methylerythritol phosphate pathway (MEP) in the chloroplast and the classical mevalonate pathway (MVA)
The 34 partial and pseudogenes separately analyzed for terpene synthase subfamily classification, where out of these, 15 partial genes falls in (terpene synthase) (TPS)-a, and 3 in TPS-b subfamily group and 1 partial gene falls in TPS-e subfamily, rest 8 pseudogenes genes fall in TPS-a subfamily, 3 in TPS-b, 2 in TPS-c, 1 in TPS-e and 1 gene in TPS-f subfamily group
Maximum pseudogenes were found among the TPS-a subfamily, after all, manual curation and sequence filtration, only 47 putative functional Ocimum sanctum terpene synthase (OsaTPS) genes were considered for further analysis Table 2
Summary
The terpenes are a large class of plant specialized secondary metabolites, which derived from 5 carbon (C5) isoprenoid unit; these precursors are produced by two biosynthetic pathways, the methylerythritol phosphate pathway (MEP) in the chloroplast and the classical mevalonate pathway (MVA). MVA is known as the isoprenoid pathway or HMG-CoA reductase pathway present in the cytosol [1,2], the pathway produces five-carbon building blocks of terpenoids called isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) [3,4], they are used to make isoprenoids. Genome wide detection of O. sanctum terpene synthase genes supported by the grants from CSIR, New Delhi networking Project BSC0121 (GENESIS) to F.K. The CIMAP Communication No is CIMAP/PUB/ 2016/80. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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