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

Authors :
Rastogi, Shubhra
Meena, Seema
Bhattacharya, Ankita
Ghosh, Sumit
Shukla, Rakesh Kumar
Sangwan, Neelam Singh
Lal, Raj Kishori
Gupta, Madan Mohan
Lavania, Umesh Chandra
Gupta, Vikrant
Nagegowda, Dinesh A
Shasany, Ajit Kumar
Source :
BMC Genomics; 2014, Vol. 15 Issue 1, p588-605, 18p, 2 Diagrams, 10 Charts, 5 Graphs
Publication Year :
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. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14712164
Volume :
15
Issue :
1
Database :
Complementary Index
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
103620529
Full Text :
https://doi.org/10.1186/1471-2164-15-588