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Open Access Highly Accessed Research article

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

Shubhra Rastogi1, Seema Meena1, Ankita Bhattacharya1, Sumit Ghosh1, Rakesh Kumar Shukla1, Neelam Singh Sangwan2, Raj Kishori Lal3, Madan Mohan Gupta4, Umesh Chandra Lavania3, Vikrant Gupta1, Dinesh A Nagegowda1* and Ajit Kumar Shasany1*

Author Affiliations

1 Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, 226015 Lucknow, U.P, India

2 Metabolic and Structural Biology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, 226015 Lucknow, U.P, India

3 Genetics and Plant Breeding Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, 226015 Lucknow, U.P, India

4 Analytical Chemistry Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, 226015 Lucknow, U.P, India

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BMC Genomics 2014, 15:588  doi:10.1186/1471-2164-15-588

Published: 12 July 2014

Abstract

Background

Ocimum 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.

Results

The 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.

Conclusion

This 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.

Keywords:
Comparative transcriptomics; Chromosome; Ocimum sanctum; Ocimum basilicum; Phenylpropanoids; Terpenoids