Browsing by Author "Bhardwaj P."

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    Adaptability of Rhododendrons in high altitude habitats
    (Northeast Forestry University, 2020) Choudhary S.; Thakur S.; Majeed A.; Bhardwaj P.
    Tree species dominate many ecosystems throughout the world and their response to climate, in light of global warming, is a matter of primary concern. This review describes past and ongoing research in Rhododendron, an ecologically important and well-adapted genus of more than 1000 species, occupying diverse habitats. Research to date indicates survival ability and mechanisms, with an emphasis on cold tolerance. The capability of long-distance gene flow in these species increases their genetic variability which in turn enhances their adaptability to newer niches as well as to environmental gradients (mainly temperature). Attempts to explain the molecular basis of morphological and behavioural changes in Rhododendron against cold-induced damage has been made. Gradual advances in 'omics' have led to an enriched genomic resource dissecting the role and interaction of multiple molecular factors participating in cold adaptability. However, fewer genetic studies are available on species with an inherent or a default cold-tolerance ability. Considering this fact, understanding specific features of an adapted species can provide insights on overriding the effects of desiccation and determining phase transitions in other plants as well. We propose to integrate ecological and evolutionary studies with functional genomics to improve predictions of tree responses to their environment.
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    Comparative analysis of metabolites in contrasting chickpea cultivars
    (Springer, 2019) Ghosh A.; Dadhich A.; Bhardwaj P.; Babu J.N.; Kumar V.
    Chickpea (Cicer arietinum L.) is a good source of nutrients for animals and human consumption. In the present study, we analyzed the anthocyanin and total phenolic contents in two contrasting (desi and kabuli) chickpea cultivars. The quantification of anthocyanins showed higher amount in desi as compared to kabuli chickpea. The total phenolic contents was estimated in desi and kabuli chickpea using two different solvents (50% Acetone and 70% Methanol extracts) for coverage of all potential phenolic compounds. In continuation, desi chickpea culitvars (himchana and ICC4958) were found to be significantly higher total phenolic contents (in both solvent extracts) as compared to kabuli cultivars (JGK-03 and L-552). Higher phenolic contents was found to be directly correlated to higher anthocyanin contents in desi as compared to kabuli chickpea. The volatile organic compounds were also analyzed using gas chromatography mass spectroscopy technique in both cultivars. The significant compositional differences in volatile organic composition (polar and non-polar) of desi and kabuli cultivars were also found to be noticed using two different solvent extractions (methanol and chloroform). The comparative analysis of volatile organic acids in methanolic and chloroform extracts of desi cultivars (himchana and ICC4958), kabuli cultivars (JGK-03 and L-552) and between desi and kabuli cultivars was also carried out for in-depth understanding of the differential patterns of low molecular weight metabolites. Six metabolites were found to be common in all four selected cultivars in chloroform extracted samples, while four were found to be common in all four selected cultivars in methanolic extracted samples. The remaining detected metabolites are uncommon among different cultivars and represented as cultivar specific signatory metabolites. In conclusion, the present investigation revealed higher anthocyanin and phenolic contents in desi cultivars as compared to kabuli cultivars and differential accumulation of volatile organic compounds in chickpea cultivars. The metabolite alterations among desi and chickpea cultivars could be the potential attribute for diversity, resilience and commercial usuages.
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    Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard
    (Canadian Science Publishing, 2019) Thakur S.; Choudhary S.; Dubey P.; Bhardwaj P.
    Arsenic is a widespread toxic metalloid that is classified as a class I carcinogen known to cause adverse health effects in humans. In the present study, we investigated arsenic accumulation potential and comparative gene expression in Indian mustard. The amount of arsenic accumulated in shoots varied in the range of 15.99–1138.70 mg/kg on a dry weight basis among five cultivars. Comparative expression analysis revealed 10 870 significantly differentially expressed genes mostly belonging to response to stress, metabolic processes, signal transduction, transporter activity, and transcription regulator activity to be up-regulated, while most of the genes involved in photosynthesis, developmental processes, and cell growth were found to be down-regulated in arsenic-treated tissues. Further, pathway analysis using the KEGG Automated Annotation server (KAAS) revealed a large-scale reprogramming of genes involved in genetic and environmental information processing pathways. Top pathways with maximum KEGG orthology hits included carbon metabolism (2.5%), biosynthesis of amino acids (2.1%), plant hormone signal transduction (1.4%), and glutathione metabolism (0.6%). A transcriptomic investigation to understand the arsenic accumulation and detoxification in Indian mustard will not only help to improve its phytoremediation efficiency but also add to the control measures required to check bioaccumulation of arsenic in the food chain.
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    Exploring microRNA profiles for circadian clock and flowering development regulation in Himalayan Rhododendron
    (Academic Press Inc., 2019) Choudhary S.; Thakur S.; Majeed A.; Bhardwaj P.
    miRNA is a non-coding, yet crucial entity in remodeling the genetic architecture. Rhododendron arboreum of Himalayas grows and even flower under fluctuating climate. sRNA from leaves of vegetative and reproductive periods was sequenced to elucidate its seasonal associations. Conserved (256) and novel (210) miRNAs and their precursors were located based on homology with plant databases and transcriptome of the species. 27,139 predicted targets were involved with metabolism, reproduction, and response to abiotic stimuli. A comparative analysis showed differential expression of 198 miRNAs with season-specific abundance of 103 miRNAs. Specific isoforms of 11 miRNA families exhibited a temporal expression and targeted different genes implying a complex regulation. The variable miRNA expression among the tissues of different conditions can be associated with the adaptability of the species, which will prove essential for further study on miRNAs mediating seasonal response. Moreover, exogenous cues also mediate phase transition via networking of flowering pathways and their components. In this context, 18 known families and 77 novel miRNAs modulating 117 genes crucial in circadian entrainment were filtered. A negative correlation was obtained between the expression of 18 of these miRNAs and their targets when tested through quantitative-PCR. It highlighted the role of miRNA-target pairs in perceiving environmental variabilities and monitoring flowering growth. Furthermore, a phylogenetic clustering was performed, which supported the lineage-specific evolution and function of putative miR156 sequence in the species. This documentation of genome-wide profiling of miRNA, their targets, and expression will enhance the understanding of developmental and climate-tolerance strategies in high-altitude trees.
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    Insights into the Molecular Mechanism of Arsenic Phytoremediation
    (Springer New York LLC, 2019) Thakur S.; Choudhary S.; Majeed A.; Singh A.; Bhardwaj P.
    Arsenic (As) is a widespread carcinogenic pollutant. Phytoremediation is the most suited technology for alleviating the As contamination of soil. In this review, we have discussed the uptake mechanism and the associated transporters for different As species. Glutathione, phytochelatins, metallothionins, and secondary metabolites play important role in As detoxification and enhancing tolerance. The roles of MAPK signaling and calcium signaling are highlighted in the perception of As stress along with phytohormones signaling in stress tolerance. Furthermore, transcription factors involved in regulation of gene expression under As stress are discussed. High-throughput sequencing has reduced the time duration and enhanced the knowledge regarding understanding the molecular mechanism of phytoremediation. The role of CRISPR/Cas9 and synthetic genes in context to phytoremediation is discussed. We have provided a holistic understanding of the present knowledge about phytoremediation in the context of mechanisms of the As uptake and tolerance. A complete understanding of the phytoremediation process is essential for As-risk mitigation and will help in augmenting its efficiency and true potential.
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    RNAseq-based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae
    (Blackwell Publishing Inc., 2019) Majeed A.; Singh A.; Choudhary S.; Bhardwaj P.
    Taxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq-based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 single-copy complete orthologous groups were selected for phylogenetic analysis. Maximum-likelihood, maximum-parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and Cephalotaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within Cephalotaxaceae.