Background: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is considered sacred by... more
Background: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and
medicinal importance in India. The common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is considered
sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report.
The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the
Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb
estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum,
Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.
Results: The pathways leading to the production of medicinally-important specialized metabolites have been
studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of
anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining
the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were
validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic
acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid,
implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.
Conclusions: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small
amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal
properties to this herb.
medicinal importance in India. The common name of this plant is ‘Tulsi’ (or ‘Tulasi’ or ‘Thulasi’) and is considered
sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report.
The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the
Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb
estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum,
Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.
Results: The pathways leading to the production of medicinally-important specialized metabolites have been
studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of
anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining
the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were
validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic
acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid,
implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.
Conclusions: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small
amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal
properties to this herb.
Research Interests:
Research Interests:
Background: Sinopodophyllum hexandrum is an endangered medicinal herb, which is commonly present in elevations ranging between 2,400–4,500 m and is sensitive to temperature. Medicinal property of the species is attributed to the... more
Background: Sinopodophyllum hexandrum is an endangered medicinal herb, which is commonly present in
elevations ranging between 2,400–4,500 m and is sensitive to temperature. Medicinal property of the species is
attributed to the presence of podophyllotoxin in the rhizome tissue. The present work analyzed transcriptome of
rhizome tissue of S. hexandrum exposed to 15°C and 25°C to understand the temperature mediated molecular
responses including those associated with podophyllotoxin biosynthesis.
Results: Deep sequencing of transcriptome with an average coverage of 88.34X yielded 60,089 assembled
transcript sequences representing 20,387 unique genes having homology to known genes. Fragments per kilobase
of exon per million fragments mapped (FPKM) based expression analysis revealed genes related to growth and
development were over-expressed at 15°C, whereas genes involved in stress response were over-expressed at 25°C.
There was a decreasing trend of podophyllotoxin accumulation at 25°C; data was well supported by the expression
of corresponding genes of the pathway. FPKM data was validated by quantitative real-time polymerase chain
reaction data using a total of thirty four genes and a positive correlation between the two platforms of gene
expression was obtained. Also, detailed analyses yielded cytochrome P450s, methyltransferases and glycosyltransferases
which could be the potential candidate hitherto unidentified genes of podophyllotoxin biosynthesis pathway.
Conclusions: The present work revealed temperature responsive transcriptome of S. hexandrum on Illumina
platform. Data suggested expression of genes for growth and development and podophyllotoxin biosynthesis at
15°C, and prevalence of those associated with stress response at 25°C.
elevations ranging between 2,400–4,500 m and is sensitive to temperature. Medicinal property of the species is
attributed to the presence of podophyllotoxin in the rhizome tissue. The present work analyzed transcriptome of
rhizome tissue of S. hexandrum exposed to 15°C and 25°C to understand the temperature mediated molecular
responses including those associated with podophyllotoxin biosynthesis.
Results: Deep sequencing of transcriptome with an average coverage of 88.34X yielded 60,089 assembled
transcript sequences representing 20,387 unique genes having homology to known genes. Fragments per kilobase
of exon per million fragments mapped (FPKM) based expression analysis revealed genes related to growth and
development were over-expressed at 15°C, whereas genes involved in stress response were over-expressed at 25°C.
There was a decreasing trend of podophyllotoxin accumulation at 25°C; data was well supported by the expression
of corresponding genes of the pathway. FPKM data was validated by quantitative real-time polymerase chain
reaction data using a total of thirty four genes and a positive correlation between the two platforms of gene
expression was obtained. Also, detailed analyses yielded cytochrome P450s, methyltransferases and glycosyltransferases
which could be the potential candidate hitherto unidentified genes of podophyllotoxin biosynthesis pathway.
Conclusions: The present work revealed temperature responsive transcriptome of S. hexandrum on Illumina
platform. Data suggested expression of genes for growth and development and podophyllotoxin biosynthesis at
15°C, and prevalence of those associated with stress response at 25°C.
Research Interests:
The non-coding elements of a genome, with many of them considered as junk earlier, have now started gaining long due respectability, with microRNAs as the best current example. MicroRNAs bind preferentially to the 3′ untranslated regions... more
The non-coding elements of a genome, with many of them considered as junk earlier, have now started gaining long due respectability, with microRNAs as the best current example. MicroRNAs bind preferentially to the 3′ untranslated regions (UTRs) of the target genes and negatively regulate their expression most of the time. Several microRNA:target prediction softwares have been developed based upon various assumptions and the majority of them consider the free energy of binding of a target to its microRNA and seed conservation. However, the average concordance between the predictions made by these softwares is limited and compounded by a large number of false-positive results. In this study, we describe a methodology developed by us to refine microRNA:target prediction by target prediction softwares through observations made from a comprehensive study. We incorporated the information obtained from dinucleotide content variation patterns recorded for flanking regions around the target sites using support vector machines (SVMs) trained over two different major sources of experimental data, besides other sources. We assessed the performance of our methodology with rigorous tests over four different dataset models and also compared it with a recently published refinement tool, MirTif. Our methodology attained a higher average accuracy of 0.88, average sensitivity and specificity of 0.81 and 0.94, respectively, and areas under the curves (AUCs) for all the four models scored above 0.9, suggesting better performance by our methodology and a possible role of flanking regions in microRNA targeting control. We used our methodology over genes of three different pathways — toll-like receptor (TLR), apoptosis and insulin — to finally predict the most probable targets. We also investigated their possible regulatory associations, and identified a hsa-miR-23a regulatory module.