Publications of NIPGR Scientists
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Item The intersection of AI and genomics in health and disease: Advancements and applications(Elsevier B.V., 2026) Kaushik, Love; Vivek, A T; Arora, Simran; Hamid, Fiza; Mukherjee, Kanka; Bisht, Niyati; Chaudhary, Sakshi; Shukla, Jagriti; Nawani, Sakshi; Kumar, ShaileshAI and genomics are revolutionizing precision medicine by using machine learning (ML) to analyze large-scale next-generation sequencing (NGS) data, identifying genetic mutations and biomarkers for personalized therapies. In practice, this accelerates drug discovery and enhances variant detection, while in cancer genomics, AI enables early detection via liquid biopsies and refines treatment by integrating multi-omics data to improve therapeutic precision. However, challenges such as data biases in underrepresented populations, limited model interpretability, and ethical concerns regarding privacy and algorithmic inequity hinder clinical adoption and demand robust governance. Efforts to diversify datasets also face standardization hurdles, although explainable AI and federated learning provide promising solutions for improving transparency and privacy. In this chapter, we discuss the role of AI in advancing genomics from diagnostics to novel therapies and emphasize the need for equitable frameworks to ensure responsible implementation, thereby paving the way for breakthroughs in personalized medicine.Item Foxtail millet (Setaria italica L.): a model for small millets(Elsevier B.V., 2023) Pramitha, Lydia; Choudhary, Pooja; Rana, Sumi; Singh, Roshan Kumar; Das, Pronomita; Sharma, Shriya; Ravikesavan, R; Prasad, Manoj; Muthamilarasan, MehanathanFoxtail millet (Setaria italica L.) is a small millet predominantly cultivated in arid and semi-arid regions of the world. India is the second-largest producer of foxtail millet, next to China, and the crop has importance in the history and civilization of the human race in these two countries. Although the foxtail millet was widely cultivated in the ancient era, it has lost its importance with time and became a marginally grown crop catering to the nutritional requirements of a limited population. Despite this, the crop has excellent yield contributing to agronomic traits along with climate-resilient characteristics. Being a C4 panicoid species with a small diploid genome, short lifecycle, in-breeding nature, and close relationship with biofuel grasses, foxtail millet has recently been considered as a C4 model crop to understand several agronomically important traits, including stress tolerance. Given the importance, the genome sequence of foxtail millet and green foxtail (S. viridis) is now available. The postgenome era has seen several crop studies, which provided extensive genetic and genomic resources for crop improvement. Studies including genetic and genomic dissection of nutritional traits, response to biotic and abiotic stresses, water-use and nitrogen-use efficiencies, biofuel traits, and deciphering the photosynthetic machinery have provided insights into the novel genes and pathways underlying the individual traits. This has also provided a roadmap for deploying similar studies in other millets using foxtail millet as a model. In this context, the chapter describes the botany, nutritional significance, global distribution, and production technologies being implemented in foxtail millet cultivation. The chapter also summarizes the outcomes of the studies being pursued to decode complex traits and provide a roadmap for executing similar work in other millet crops.Item PtRNAdb: a web resource of plant tRNA genes from a wide range of plant species(Springer Nature Publishing AG, 2022) Singh, Ajeet; Zahra, Shafaque; Das, Durdam; Kumar, ShaileshtRNA, as well as their derived products such as short interspersed nuclear elements (SINEs), pseudogenes, and transfer RNA (tRNA)-derived fragments (tRFs), have now been shown to be vital for cellular life, functioning, and adaptation during different stress conditions in all diverse life forms. In this study, we have developed PtRNAdb (www.nipgr.ac.in/PtRNAdb), a plant-exclusive tRNA database containing 113,849 tRNA gene sequences from phylogenetically diverse plant species. We have analyzed a total of 106 nuclear, 89 plastidial, and 38 mitochondrial genomes of plants by the tRNAscan-SE software package, and after careful curation of the output data, we integrated the data and developed this database. The information about the tRNA gene sequences obtained was further enriched with a consensus sequence-based study of tRNA genes based on their isoacceptors and isodecoders. We have also built covariance models based on the isoacceptors and isodecoders of all the tRNA sequences using the infernal tool. The user can also perform BLAST not only against PtRNAdb entries but also against all the tRNA sequences stored in the PlantRNA database and annotated tRNA genes across the plant kingdom available at NCBI. This resource is believed to be of high utility for plant researchers as well as molecular biologists to carry out further exploration of the plant tRNAome on a wider spectrum, as well as for performing comparative and evolutionary studies related to tRNAs, and their derivatives across all domains of life. Database URL: http://www.nipgr.ac.in/PtRNAdb/Item Genomics approaches to synthesis plant-based biomolecules for therapeutic applications to combat SARS-CoV-2(Elsevier B.V., 2020) Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Ashish; Prasad, ManojCOVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.Item The genome sequence of segmental allotetraploid peanut Arachis hypogaea(Springer Nature Publishing AG, 2019) Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal-Bertioli, Soraya C. M.; Ren, Longhui; Farmer, Andrew D.; Pandey, Manish K.; Samoluk, Sergio S.; Abernathy, Brian; Agarwal, Gaurav; Ballén-Taborda, Carolina; Cameron, Connor; Campbell , Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; Baidouri, Moaine El; Guo, Baozhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher G.; Mirouze, Marie; Moretzsohn, Márcio C.; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, Erez L.; Michelmore, Richard; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K. S.; Scheffler, Brian E.; Grimwood, Jane; Ozias-Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz , JeremyLike many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.Item Millets genetic engineering: the progress made and prospects for the future(Springer Nature, 2019) Sood, Priyanka; Singh, Roshan Kumar; Prasad, ManojSustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective(Elsevier B.V., 2019) Muthamilarasan, Mehanathan; Singh, Nagendra Kumar; Prasad, ManojFor several decades, researchers are working toward improving the “major” crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing “integrating omics” for gaining a better understanding of crops' response to abiotic and biotic stresses.Item Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes(Springer Nature, 2019) Jha, Uday Chand; Bohra, Abhishek; Jha, Rintu; Parida, Swarup K.Key message Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Abstract Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on ‘adaptive traits’ that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping–genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated “omics-assisted” approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp ISTKB(BioMed Central Ltd, 2018) Kumar, Madan; Verma, Sandhya; Gazara, Rajesh Kumar; Kumar, Manish; Pandey, Ashok; Verma, Praveen K.; Thakur, Indu ShekharBackground: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA Conclusions: The unusual aerobic'-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total seguenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches providedvalidation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.Item Production and characterization of polyhydroxyalkanoate from lignin derivatives by Pandoraea sp. ISTKB(American Chemical Society, 2017) Kumar, Madan; Singhal, Anjali; Verma, Praveen Kumar; Thakur, Indu ShekharThe present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain Pandoraea sp. ISTKB. PHA production was screened by fluorescence microscopy and flow cytometry using a Nile red stain. PHA and biomass accumulation, while screening, was found to be maximum on 4-hydroxybenzoic acid followed by p-coumaric acid, vanillic acid, 2,6-dimethoxyphenol, and kraft lignin after 96 h. Monomer composition was analyzed by gas chromatography–mass spectrometry (GC–MS) and was followed by Fourier transform infrared and 1H NMR analysis, indicating PHA to be a copolymer of P(hydroxybutyrate-co-hydroxyvalerate). Genomic analysis of Pandoraea sp. ISTKB also complemented the results of GC–MS and NMR, and the relevant genes responsible for the synthesis of small chain length PHA were discovered in the genome. Process parameters were optimized by response surface methodology for enhanced production of PHA and biomass on 4-hydroxybenzoate. Optimization results showed 30 and 66% increase in the biomass and PHA production, respectively. The results obtained were promising and indicated that if lignin is depolymerized into low-molecular-weight intermediates, then it can easily be utilized and converted into value-added products like PHA by microbes.