Publications of NIPGR Scientists

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    AtFusionDB: A comprehensive database of fusion transcripts in model plant Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Shree, Tanu; Kumar, Shailesh
    Fusion transcripts are chimeric RNAs, produced by the joining of two different RNAs at the RNA level or as a product of gene fusion at the DNA level. In this era of high-throughput sequencing technologies, it is easy to identify novel molecules like fusion transcripts in different systems. That's because, initially, supposed to be the well-known cancer biomarkers, fusion transcripts are also validated in normal human physiology. In Planta, discrete reports are available, indicating the presence of fusion transcripts but no dedicated web resource is available for the plant-specific fusion transcripts. This chapter describes the first plant-specific database of fusion transcripts, i.e., AtFusionDB ( http://www.nipgr.res.in/AtFusionDB ), which contains the information on fusion transcripts identified in the model plant Arabidopsis thaliana. This database can be exploited to get significant information about gene/transcript fusion in plants.
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    Validation of plant fusion peptides using proteomics data
    (Springer Nature Publishing AG, 2026) Hamid, Fiza; Aftab, Sahrish; Shree, Tanu; Kumar, Shailesh
    Fusion transcripts and their fused protein products are emerging as exciting entities in molecular biology, offering potential applications in diagnostics and therapeutics. These fusion proteins, derived from the translation of fusion transcripts, hold promise as unique biomarkers and targets for intervention. While numerous algorithms exist to identify fusion RNAs, the detection and validation of their protein counterparts through proteomics remains a growing area of research. This challenge is particularly intriguing in plant biology, where fusion events may affect stress responses, development, and adaptation. This chapter provides an accessible and practical workflow for validating plant fusion peptides using publicly available proteomics datasets.
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    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, Shailesh
    tRNA, 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/
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    PtRFdb: Plant tRNA-derived fragments database
    (Springer Nature Publishing AG, 2019) Zahra, Shafaque; Kumar, Shailesh
    The transfer RNA-derived fragments or tRFs represent a distinct class of small non-coding RNAs, and have been detected in evolutionarily divergent organisms. The role of tRFs in human cancers and infectious diseases as well as in gene regulation has been well established in diverse organisms. However, in plants, there is a need to further consolidate the tRF research by identification and characterization of tRFs because this domain is still unexplored across the plant kingdom. This chapter discusses about PtRFdb (www.nipgr.res.in/PtRFdb), a web-based repository harbouring the valuable information related to transfer RNA derived fragments (tRFs) in 10 different plant species. This database is believed to be beneficial for molecular biologists in facilitating future survey and characterization of tRFs across the plant kingdom.