title: De novo sequencing and comparative analysis of holy and sweet basil transcriptomes.
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.
  
  
  CONCLUSIONS
  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.
authors.forename: Shubhra
authors.initials: S
authors.lastname: Rastogi
authors.forename: Seema
authors.initials: S
authors.lastname: Meena
authors.forename: Ankita
authors.initials: A
authors.lastname: Bhattacharya
authors.forename: Sumit
authors.initials: S
authors.lastname: Ghosh
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Shukla
authors.forename: Neelam Singh
authors.initials: NS
authors.lastname: Sangwan
authors.forename: Raj Kishori
authors.initials: RK
authors.lastname: Lal
authors.forename: Madan Mohan
authors.initials: MM
authors.lastname: Gupta
authors.forename: Umesh Chandra
authors.initials: UC
authors.lastname: Lavania
authors.forename: Vikrant
authors.initials: V
authors.lastname: Gupta
authors.affiliation: Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, 226015 Lucknow, U,P, India. da.nagegowda@cimap.res.in.
authors.forename: Dinesh A
authors.initials: DA
authors.lastname: Nagegowda
authors.forename: Ajit Kumar
authors.initials: AK
authors.lastname: Shasany
mesh_terms: D055028:Comparative Genomic Hybridization; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008798:Mevalonic Acid / Q000737:chemistry / Q000378:metabolism; D058977:Molecular Sequence Annotation; D031339:Ocimum / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013729:Terpenes / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D013729:Terpenes; D014157:Transcription Factors; D003577:Cytochrome P-450 Enzyme System; D008798:Mevalonic Acid