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De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L.

Published online by Cambridge University Press:  02 December 2021

Tanuja ,
Nibir Ranjan Parasar ,
Ravichandiran Kumar ,
Purushothaman Natarajan  and
Madasamy Parani Open the ORCID record for Madasamy Parani [Opens in a new window]
Tanuja
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Nibir Ranjan Parasar
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Ravichandiran Kumar
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
Purushothaman Natarajan
Affiliation:
Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, USA
Madasamy Parani*
Affiliation:
Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
*
Author for correspondence: Madasamy Parani, E-mail: paranim@srmist.edu.in
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Abstract

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Keywords

Basilde novo assemblyOcimum gratissimumRNA sequencingtranscriptome
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 6 , December 2021 , pp. 469 - 476
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

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