De novo sequencing and comparative analysis of holy and sweet basil transcriptomes

Abstract

BackgroundOcimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing.ResultsThe sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.ConclusionThis is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-588) contains supplementary material, which is available to authorized users.

Virus‐induced gene silencing of Withania somnifera squalene synthase negatively regulates sterol and defence‐related genes resulting in reduced withanolides and biotic stress tolerance

“…RNA isolation, cDNA synthesis and qPCR analysis were performed as reported previously (Rai et al, 2013;Rastogi et al, 2014). For semi-quantitative RT-PCR, 18S rRNA gene served as an endogenous control for RNA quantity.…”

Rapid detection of Fusarium wilt in basil (Ocimum sp.) leaves by desorption electrospray ionization mass spectrometry (DESI MS) imaging

“…1A The leaves of O. tenuiorum and O. basilicum look similar and have to be differentiated based on the colors of their inorescences ( Fig. 24 In this study, the characteristic predominant peaks for each species of basil are unique (for example m/z 349 for O. gratissimum, m/z 378 for O. tenuiorum and m/z 201 for O. basilicum), which were used as markers to identify each basil species in further experiments. The advantage of DESI MS imaging is that the molecular differences can be identied at any stage of plant growth, without waiting for the owering stage; here the molecular similarities and differences were understood by comparing the predominant peaks of both species of O. tenui-orum and O. basilicum ( Fig.…”

The Holy Basil (<I>Ocimum sanctum</I> L.) and its Genome

“…The chromosome number of this plant was analyzed to be 2n=16 (Rastogi et al, 2014). Approximately, 80% of the patents on Ocimum sp.…”