NIPGR, New Delhi
Unraveling the Secrets of Plant Genomics and Regulatory Networks: Pioneering Computational studies to identify Novel RNA Molecules for Crop Improvement at NIPGR"
The Bioinformatics Center at DBT-NIPGR, New Delhi is actively involved in developing diverse tools and databases dedicated to plant genome research. It focuses on identifying and characterizing novel components within genome regulatory circuits in plants, including molecules such as tRNA fragments, fusion transcripts, and novel gene families. tRNA-derived non-coding RNAs (tncRNAs) and fusion transcripts play crucial roles in governing genome regulatory circuits, with their expression undergoing significant changes during stress conditions. This provides an avenue to regulate gene expression by targeting these molecules. Leveraging these discoveries, the center aims to enhance crops by generating transgenic lines utilizing these molecules. Additionally, the composition of metabolites significantly influences a plant's phenotype and its ability to adapt to the environment, directly impacting the nutritional value of plant produce. However, the metabolic pathways in crops remain largely unexplored, offering an untapped area for further investigation.
In response, the center has set specific objectives that include understanding the evolution and domestication of crop plants, defining the switches within gene regulatory networks, exploring the function of tRNA-derived RNA fragments, characterizing fusion transcripts in plants, and developing bioinformatics resources for genomics-assisted breeding. These objectives serve as focal points guiding the center's efforts to uncover the intricacies of crop genetics and advance methods for crop improvement through informed breeding practices.
The workflow used for developing PTPAMP, a prediction tool to predict the presence of antimicrobial activity of plant-derived peptides
Plant transfer RNA-derived non-coding RNAs (tncRNAs) database
The center's achievements stand out, particularly with the creation of the ‘tncRNA Toolkit’, a software designed specifically for identifying tRNA fragments, coupled with the development of PtncRNAdb, a comprehensive database dedicated to these fragments. These resources are crucial tools widely utilized by the scientific community for further investigations into genome regulation in plants. Moreover, the center has established the first-ever database and tool tailored specifically for tRNA and rRNA fragments. Equipped with a robust computational infrastructure comprising two high- performance computing (HPC) systems from HPE and Lenovo, the center ensures cutting-edge capabilities essential for groundbreaking bioinformatics research in plant genomics.
In the National Network Project (NNP), NIPGR will delve into both existing and novel rice and chickpea NGS data sets, aiming to elucidate diverse metabolic pathways linked to critical traits. Collaboratively, NIPGR and Ashoka University will delineate regulatory switches of genetic networks of specific metabolites. Simultaneously, IIRR will explore epigenomics data to characterize epialleles associated with agronomically important metabolic pathways in rice. Additionally, IISR will undertake transcriptome analysis of black pepper, decoding its varied metabolic pathways. Together, the network project aims to generate new information in unexplored areas of agronomically important metabolic pathways in rice, chickpeas, and black pepper. The center proposes to create user-friendly public web databases with current and newly available information for these crops.
