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Holy basil decoded

Holy basil or tulsi is for long known to be a wonder herb. In a first of sorts, a scientist decodes its genome to lend more credence to its medicinal value. He shares more insights with Shalini Gupta

Holy basil or tulsi is for long known to be a wonder herb. In a first of sorts, a scientist decodes its genome to lend more credence to its medicinal value. He shares more insights with Shalini Gupta

20150630ep29In a breakthrough research, a scientist from Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP), Lucknow, has published whole genome sequence of Ocimum sanctum, also known as  ‘Holy basil’ or ‘Tulsi’, revered as ‘Vishnupriya’ and worshipped for over more than 3000 years through the sacred traditions of Hindu culture. This is the first report of the complete genome sequence of the plant, using composite next generation sequencing technologies.  Not only is this the first step to understand and unravel the secrets of this ‘mother of all herbs’, but will also provide scientific validity to the traditional claims of its medicinal usage.

Dr AK Shasany, a principal senior scientist from the biotechnology division of CIMAP, who is behind this development, has been curious about the herb since a very long time. Talking about it, he says, “Since tulsi has been a repository of a plethora of biochemicals and finds a distinguished place in all the ancient traditional medicinal systems including Ayurveda, Greek, Unani and Roman, I was curious. My inquisitiveness increased when I started the literature survey of the genes responsible for the biosynthesis of the important medicinal compounds. I found that very less data was available for holy basil as far as the molecular biology studies were concerned; major studies were based on the chemical profiling and the biological activity testing of the plant.” This is what triggered his interest into an in-depth study.


‘Patents need novelty, non obviousness and commercial utility’

20150630ep30The patent of turmeric to US got annulled and appeared as a headline in the  a daily newspaper, dated January 28, 2013 that “India foils US firm bid to patent turmeric”. This was possible with the help of The Traditional Knowledge Digital Library (TKDL), a unit of Council of Scientific & Industrial Research (CSIR) which is repository of prior submitted art evidences in the form of references in  books from 18th century to the 20th century citing evidences that turmeric, apple, basil, kalamegha and licorice have been used alone or in combination with a few other ingredients for the treatment of inflammation, psoriasis, gastritis and as anti-inflammatory in the Indian systems of medicine. Patents need novelty, non obviousness and commercial utility. I wonder how the composition of re-blend of two known compounds of turmeric reported by Kerala-based company got that patent approved as it again was based on the medicinal properties that already are well known in Indian traditional knowledge. I’m also aware of the patent granted to the Avesthagen was revoked in 2012 by the Indian Government against the composition for treatment of diabetes. The composition consisted of jamun, lavangpatti and chandan came under attack in view of public interest under section 66 of the Patent Act, 1970 and also because the patent infringed upon the TKDL of India. Considering these examples, I feel that there should be stringent laws and learned patent experts to keep a check on those who defy the patent laws. We already have a US patent for the variety ‘CIM-AYU’ which was used for the whole genome sequencing. Genome sequence cannot be patented as such, but can be used by all to validate the properties of tulsi. Hence, the revered plant of our country will reach more populations of the world.

Dr AK Shasany, Principal Senior Scientist Biotechnology Division, CIMAP


He has significantly contributed to analysing genomes of more than 900 accessions belonging to 40 different plant species for genetic diversity estimation, evolutionary relationships and marker identification. He is also responsible for the release of 33 commercially important varieties with 22 US plant patents, using genomics as well as breeding tools. His contribution in research related to Mentha and Artemisia won CIMAP technology awards in 1999 and 2012. He isolated and determined the function of several novel genes from medicinal and aromatic plants and is also associated in determining the efficacy and mechanism of action for novel uses of phytomolecules, leading to different product formulations having economic/ commercial importance. He has collaborated with CDRI and SGPGI to understand the antigen proteins of several pathogens with the objective to use those for targets to screen plant compounds for human health. Shasany combines his understanding on plant diversity for identifying economically important genotypes for conservation, cultivation and understanding metabolic biology including the applied aspect of MAPs on human health and benefits.

He started his professional career after graduating from Indian Agricultural Research Institute (PhD. Molecular Biology and Biotechnology) along with a Post-Doctoral degree from Purdue University, US. He also secured highest Overall Grade point average(OGPA) (8.81/10.00) in MSc with two awards and studied Agricultural Biotechnology. Having a Bachelor’s degree in Agriculture and trained in National Academy of Agricultural Research Management (NAARM) as an ARS (ICAR) scientist, he blends very well with recent approaches on plant molecular biology. His research interest includes, plant diversity, metabolic engineering in medicinal and aromatic plants and bioprospection for human health.


Achievements

  • Total publications: 117 (International: 60); Citations: 1730 (Google Scholar)
  • Cumulative Impact factor: More than 164.28
  • Granted US Patents: 50 (DNA sequences 3, Plants 22, 10 processes, 15 compositions).
  • Variety Development: 38 (Most of the plants are now cultivated by the farmers).
  • Involved in 30 projects from which led 16 projects as  Principal Investigator/Co-PI. Principal Investigator for major CSIR project NWP 008 (11th Plan, System biology), BSC0203 (12th Plan, Aroma Genomics).
  • Now leading the major project ChemBio of CSIR-CIMAP

The genome of holy basil, assembled de novo in this study, presents the smallest nuclear genome in the family Lamiaceae (386 Mb) and smallest chroloplast genome in the order Lamiales (142,245 bp). A total of 107,785 contigs were assembled into 22,776 scaffolds and finally super-scaffolding after gap-closing resulted in 9059 super – scaffolds. Out of 85,723 protein coding loci from a total of 53,480 got annotated, but only 22,270 protein coding genes were found to be unique and the rest are of unknown function.  136 proteins were identified as homologous to five important plant genomes with 142,601 simple sequence repeats (SSRs) predicted, with the highest being mono-repeats. The pathway analysis indicated an abundance of phenylpropanoids while phylogenetic analysis for chloroplast proteome placed Salvia miltiorrhiza as the nearest neighbour. Although, both these plants predominantly produce phenylpropanoids, and both have the identical diploid number of chromosomes (2n = 16), the genome size of O. sanctum (386 Mb) is a little more than half of the genome size of S. miltiorrhiza indicating that O. sanctum genome is more compact than that of S. miltiorrhiza.

The availability of the genome sequence now opens the possibility to identify genes involved in producing therapeutic molecules and to produce them in vitro. This will also facilitate identification of not yet identified genes involved in the synthesis of important secondary metabolites in this plant. Elaborates Shasany, “The presence of large number of homologs of certain protein coding genes in genome indicates the possibility of finding newer biomolecules having potential bioactivity not implicated so far. The genomic information generated in this investigation not only is an important resource for evolutionary studies but will also catalyse modern genetic research by augmenting the data available for plant comparative genomics, thus accelerating identification of important secondary metabolite-synthesising genes, not identified yet from this medicinal and aromatic plant.


Awards

  • Dr Kumud Chandra Bora Memorial award for securing highest Overall Grade Point Average in M.Sc. (Agcultural Biotechnology)
  • Prof Deveswar Pathak Memorial award, for securing highest Overall Grade Point Average in M.Sc. (Agriculture)
  • IARI Merit medal for outstanding Academic performance during Ph.D Molecular Biology and Biotechnology (1996)
  • CSIR Technology prize for Biological sciences and Technology (1999), for  development of early maturing disease and pest resistant menthol mint
  • CSIR-Technology Awards 2012 for Biological sciences, Development and commercialisation of anti-malarial drug plant Artemisia annua technology package facilitating industrial growth, societal health and rural prosperity
  • CSIR young scientist award in biological sciences (2000) for research on mint
  • Prof Umakant Sinha Memorial award (Indian Science Congress Association) 2003, for genome analysis and IPR protection

“Specific pathway related genes identified or mined in this genome could be used for the production of secondary metabolites following synthetic biology approaches, as well as genetic markers developed based on these genome sequences for studies involving genetic map construction, positional cloning, strain identification and marker – assisted selection. These molecular tools and genomic resources will accelerate molecular breeding and ultimately holy basil’s utility in medical community”, he adds.

The draft National Health Policy 2015 suggests greater integration of AYUSH with modern medicine, a type of ‘cross-pathy’ that the Indian Medical Association has strongly opposed. Recently, it has also been suggested that traditional medicine needs to be more evidence based in order to reaffirm its effectiveness. “As allopathy emerged, it stole all the attention from all other medical treatments as it gave fast results. Everyone wants to have a faster recovery from their ailments. However, as people get aware of the side effects and the long term effects of allopathic treatments, they are again  towards the traditional medical treatments. Our age-old medicinal system developed on the basis of practice and experience. But, today for better acceptability of this medicine all over the world, we need scientific validation and more evidence  to spread of these medicinal systems beyond Indian boundaries,” he stresses.

shalini.g@expressindia.com

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