Publications of NIPGR Scientists
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Item Reimagining plant science training in the era of generative AI: A global perspective(Oxford University Press, 2026) Moghe, Gaurav; Zimic-Sheen, Alen; Chen, Dijun; Yadav, Gitanjali; Cao, Guangshuo; Tufan, Hale; Williams, Jason; Szymański, Jędrzej; Kim, Jeongwoon; Busta, Lucas; Mutwil, Marek; Verdu, Miguel; Zimic, Mirko; Provart, Nicholas J; Makunga, Nokwanda; Wilkins, Olivia; Sun, Qi; VanBuren, Robert; Marks, Rose A; Rhee, Seung Y; Jiang, Yu; Xie, YuyingIn recent years, a deluge of big and diverse datasets from hundreds of plant species coupled with spectacular innovations in artificial intelligence (AI) and generative AI (GenAI), has altered the landscape of plant science. These developments are increasingly democratizing the field, reducing the entry barriers to complex data analysis and enabling a new wave of innovative research while introducing new challenges. Therefore, in this era, it is critical that we train the next generation of plant scientists to be AI-literate, i.e., not only proficient in using AI but also vigilant about its pitfalls and biases. In this Perspective, we call for six strategic shifts necessary for training the next generation of plant scientists. We argue that while maintaining a core focus on subject expertise, educators should simultaneously emphasize development of new AI-forward pedagogical and evaluation frameworks that reward interdisciplinary and critical thinking, human-driven knowledge synthesis, self-directed learning, and conceptual understanding of workflows. For effective critique and sound interpretations based on biological reality, plant scientists must be explicitly trained in recognizing biases underlying GenAI models. Finally, we highlight the structural barriers hindering the equitable and ethical use of GenAI, where awareness and resolution is critical for sustainable growth of the field. Through the above conceptual framework and numerous plant-science focused illustrative activities, examples, and resources meant for students and educators alike, this Perspective defines high-level emphasis areas for GenAI-enabled scientific training, aimed at creating a more effective, engaged, and adaptive community of plant scientists.Item Global bibliometry on three decades of methyl jasmonate-induced plant defense research reveals growth of a specialty area in biology(Open Science Publishers LLP, 2025) Chugh, Vipul; Kumari, Kamlesh; Yamal, Gupta; Checker, Vibha Gulyani; Yadav, Gitanjali; Kathpalia, RenuMethyl jasmonate (MeJA), a naturally existing plant hormone, acts as a vital defense and signaling molecule. Although this hormone has been discovered recently, published reports spanning the last several decades have shown the pleiotropic effects of the hormone raising numerous questions about its regulation, biogenesis, and mode of action. In this work, we explore the complete scientific research on MeJa from its discovery in 1992, spanning research conducted over three decades, through a complex network analysis of 2,542 documents authored by about 9,000 individuals. Several indicators of research progress were evaluated, including co-authorship networks, keyword thematic maps, indices of national and international collaboration, annual scientific production, and most productive affiliations. These indices not only enabled us to evaluate the importance of a specialty discipline in literature but also the place of nations in determining research directionality and the significance of quality of work. Overall, this bibliometric analysis identifies current research trends in a specialty area in biology and we hope that our work would pave the way for greater international collaborations among researchers and a better understanding of research gaps and future scope of work in the actively expanding field of MeJA induced plant defense, stress, and developmental processes.Item Editorial: Plant transcription factors associated with abiotic stress tolerance in crops and wild-relatives(Frontiers Media S.A., 2024) Puglia, Giuseppe Diego; Frugis, Giovanna; Yadav, GitanjaliEditorial on the Research Topic Plant transcription factors associated with abiotic stress tolerance in crop and wild-relatives Global climate change (GCC), by altering the intensity and frequency of potentially damaging weather events such as droughts, waterlogging, heat waves, and cold spells, has altered seasonal weather patterns, causing severe problems for plant crops and wildlife species (Cramer et al., 2011; Asseng et al., 2015; Minoli et al., 2019). To cope with these challenges, plants have evolved complex regulatory mechanisms that enable them to respond and adapt to changing environmental conditions, while maintaining a balance between optimal growth and stress (Eckardt et al., 2023). This Research Topic brings together several contributions that highlight the role of transcriptional regulation in plant responses to abiotic stresses and hypothesise its role in stress tolerance. The studies published in this Research Topic deal with well-recognised groups of transcription factors (TFs), but also with new ones whose association with the response to abiotic stresses has been demonstrated by recent molecular advances. This evidence allows us to shed light on the mechanisms by which plants respond to different stresses, with a focus on abiotic stresses such as salt, drought, cold, and waterlogging.Item Role of transcriptional regulation in auxin-mediated response to abiotic stresses(Frontiers Media S.A., 2024) Marzi, Davide; Brunetti, Patrizia; Saini, Shashank Sagar; Yadav, Gitanjali; Puglia, Giuseppe Diego; Dello, Ioio RaffaeleGlobal climate change (GCC) is posing a serious threat to organisms, particularly plants, which are sessile. Drought, salinity, and the accumulation of heavy metals alter soil composition and have detrimental effects on crops and wild plants. The hormone auxin plays a pivotal role in the response to stress conditions through the fine regulation of plant growth. Hence, rapid, tight, and coordinated regulation of its concentration is achieved by auxin modulation at multiple levels. Beyond the structural enzymes involved in auxin biosynthesis, transport, and signal transduction, transcription factors (TFs) can finely and rapidly drive auxin response in specific tissues. Auxin Response Factors (ARFs) such as the ARF4, 7, 8, 19 and many other TF families, such as WRKY and MADS, have been identified to play a role in modulating various auxin-mediated responses in recent times. Here, we review the most relevant and recent literature on TFs associated with the regulation of the biosynthetic, transport, and signalling auxin pathways and miRNA-related feedback loops in response to major abiotic stresses. Knowledge of the specific role of TFs may be of utmost importance in counteracting the effects of GCC on future agriculture and may pave the way for increased plant resilience.Item Cavity architecture based modulation of ligand binding tunnels in plant START domains(Elsevier B.V., 2023) Mahtha, Sanjeet Kumar; Kumari, Kamlesh; Gaur, Vineet; Yadav, GitanjaliThe Steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain represents an evolutionarily conserved superfamily of lipid transfer proteins widely distributed across the tree of life. Despite significant expansion in plants, knowledge about this domain remains inadequate in plants. In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. We validate 28 rice START domain models, delineate binding cavities, measure pocket volumes, and compare these with mammalian counterparts to understand evolution of binding preferences. Overall, plant START domains retain the ancestral α/β helix-grip signature, but we find subtle variation in cavity architectures, resulting in significantly smaller ligand-binding tunnels in the plant kingdom. We identify cavity lining residues (CLRs) responsible for reduction in ancestral tunnel space, and these appear to be class specific, and unique to plants, providing a mechanism for the observed shift in domain function. For instance, mammalian cavity lining residues A135, G181 and A192 have evolved to larger CLRs across the plant kingdom, contributing to smaller sizes, minimal STARTs being the largest, while members of type-IV HD-Zip family show almost complete obliteration of lipid binding cavities, consistent with their present-day DNA binding functions. In summary, this work quantifies plant START structural & functional divergence, bridging current knowledge gaps.Item Quantification of pollen viability in Lantana camara by digital holographic microscopy(Cambridge University Press, 2023) Kumar, Vipin; Goyal, Nishant; Prasad, Abhishek; Babu, Suresh; Khare, Kedar; Yadav, GitanjaliPollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.Item Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism(Oxford University Press, 2022) Verma, Prabha; Kumari, Poonam; Negi, Shreya; Yadav, Gitanjali; Gaur, VineetHolliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.Item Ecological networks in urban forest fragments reveal species associations between native and invasive plant communities(MDPI AG, 2022) Chauhan, Sonali; Yadav, Gitanjali; Babu, SureshForest fragments are characteristic features of many megacities that have survived the urbanisation process and are often represented by unique assemblages of flora and fauna. Such woodlands are representations of nature in the city—often dominated by non-native and invasive species that coexist with resilient native congeners and purposefully introduced flora. These forest fragments also provide significant ecosystem services to urban society and therefore, understanding their compositional patterns is of considerable importance for conservation and management. In this work, we use a complex network approach to investigate species assemblages across six distinct urban forest fragments in the South Delhi Ridge area of the National Capital Territory, India. We generate bipartite ecological networks using conventional vegetation sampling datasets, followed by network partitioning to identify multiple cliques across the six forest fragments. Our results show that urban woodlands primarily form invasive–native associations, and that major invasive species, such as Prosopis juliflora and Lantana camara exclude each other while forming cliques. Our findings have implications for the conservation of these urban forests and highlight the importance of using network approaches in vegetation analysis.Item Arabidopsis target of rapamycin coordinates with transcriptional and epigenetic machinery to regulate thermotolerance(Frontiers Media S.A., 2021) Sharma, Mohan; Jamsheer, K.M.; Shukla, Brihaspati Narayan; Sharma, Manvi; Awasthi, Prakhar; Mahtha, Sanjeet Kumar; Yadav, Gitanjali; Laxmi, AshveryaGlobal warming exhibits profound effects on plant fitness and productivity. To withstand stress, plants sacrifice their growth and activate protective stress responses for ensuring survival. However, the switch between growth and stress is largely elusive. In the past decade, the role of the target of rapamycin (TOR) linking energy and stress signalling is emerging. Here, we have identified an important role of Glucose (Glc)-TOR signalling in plant adaptation to heat stress (HS). Glc via TOR governs the transcriptome reprogramming of a large number of genes involved in heat stress protection. Downstream to Glc-TOR, the E2Fa signalling module regulates the transcription of heat shock factors through direct recruitment of E2Fa onto their promoter regions. Also, Glc epigenetically regulates the transcription of core HS signalling genes in a TOR-dependent manner. TOR acts in concert with p300/CREB HISTONE ACETYLTRANSFERASE1 (HAC1) and dictates the epigenetic landscape of HS loci to regulate thermotolerance. Arabidopsis plants defective in TOR and HAC1 exhibited reduced thermotolerance with a decrease in the expression of core HS signalling genes. Together, our findings reveal a mechanistic framework in which Glc-TOR signalling through different modules integrates stress and energy signalling to regulate thermotolerance.Item StAR-related lipid transfer (START) domains across the rice pangenome reveal how ontogeny recapitulated selection pressures during rice domestication(Frontiers Media S.A., 2021) Mahtha, Sanjeet Kumar; Purama, Ravi Kiran; Yadav, GitanjaliThe StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.