Institutional Publications

Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11

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Author: search.filters.author.Sahu, Namrata

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    AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes
    (Elsevier B.V., 2026) Shukla, Jagriti; Mukherjee, Kanka; Sahu, Namrata; Kumar, Shailesh
    The rapid expansion of publicly available genome assemblies has made genome annotation an increasingly challenging task, particularly for large-scale analyses across prokaryotic and eukaryotic organisms. While several tools exist for assembly evaluation and annotation, their use often involves fragmented workflows that require extensive manual coordination. To overcome this limitation, we introduce AquaaG, an automated and reproducible genome annotation pipeline. AquaaG integrates genome assembly retrieval from NCBI, assembly quality assessment using QUAST, organism-specific annotation using Prokka for prokaryotes and BRAKER3 for eukaryotes, gene-space completeness evaluation using BUSCO, and functional annotation using EggNOG-mapper. The pipeline is configured through simple YAML files and supports species-level, kingdom-level, and custom assembly-based analyses with optional submitter-based filtering. AquaaG therefore provides a practical and reproducible framework for high-throughput genome annotation and assessment.
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    AraNSdb: a dedicated database of stress-responsive non-coding RNAs in Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, A.T.; Bhatia, Manika; Sahu, Namrata; Kalakoti, Garima; Kaushik, Love; Mukherjee, Kanka; Kumar, Shailesh
    Plants, as sessile organisms, are constantly exposed to biotic and abiotic stresses, making their ability to respond crucial for survival. Non-coding RNAs (ncRNAs) have emerged as key regulators in these stress responses, with several studies identifying numerous stress-responsive ncRNAs (SRNs). However, a comprehensive collection of SRNs derived from sequencing data in Arabidopsis thaliana has been lacking. To address this, we utilized high-throughput experimental data and mined published studies to construct AraNSdb (Arabidopsis ncRNA Stress Database), a systematic resource for storing and querying SRNs. AraNSdb documents over 1,000 expression profiles from diverse stress datasets, encompassing 6,616 SRNs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The database features an intuitive web interface for exploring SRNs associated with specific stress types and provides detailed ncRNA annotations to support functional and regulatory studies. AraNSdb offers a valuable platform for advancing our understanding of ncRNA-mediated stress responses and is freely accessible at http://www.nipgr.ac.in/AraNSdb.
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    Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, AT; Kiran, Harikumar; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Background:- Long non-coding RNAs (lncRNAs) play key roles in regulating plant growth, development, and stress responses. Despite their increasing identification in plant transcriptomes, a systematic characterization of lncRNAs is still lacking, leaving a significant knowledge gap. To address this, we systematically identified and characterized Arabidopsis lncRNAs through integrative analysis of strand-specific RNA sequencing data and multi-omics datasets, revealing their genomic features, regulatory interactions, and evolutionary characteristics. Results:- Using a custom pipeline applied to hundreds of stranded RNA-seq datasets, we assembled a comprehensive catalog of 4,772 intergenic and antisense Arabidopsis lncRNAs. In comparing multiple key features of lncRNAs with those of protein-coding genes, we found that intergenic lncRNAs contain high transposable element-derived fragments and display broader TE diversity. Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes. We additionally uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation, with a minor subset classified as Pol V–transcribed. Of note, our results revealed lncRNAs mediating stress-responsive cis interactions and others linked to trait-associated loci. Probing further, an experimental evidence resource confirmed small peptide production from multiple lncRNA loci. Extending our investigation, comparative analyses across Brassicaceae species revealed syntenic lncRNAs enriched for shared sequence motifs despite substantial sequence divergence. Conclusions:- This study provides a valuable and extensively annotated catalog of Arabidopsis lncRNAs, revealing their diverse genomic features, regulatory interactions, and evolutionary characteristics. Altogether, our work advocates for multi-omics integrative analysis as a potent strategy to efficiently enhance lncRNA annotation, providing insights into functionality and addressing annotation limitations. Our comprehensive bioinformatic analyses of Arabidopsis lncRNAs pave the way for future functional characterization of these transcripts.
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    ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana
    (Elsevier B.V., 2025) Vivek, AT; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Eukaryotic transcriptomes are remarkably complex, encompassing not only protein-coding RNAs but also an expanding repertoire of noncoding RNAs (ncRNAs). In plants, ncRNA-ncRNA interactions (NNIs) have emerged as pivotal regulators of gene expression, orchestrating development and adaptive responses to stress. Despite their critical roles, the functional significance of NNIs remains poorly understood, largely due to a lack of comprehensive resources. Here, we present ANNInter, a comprehensive platform that integrates computational predictions with experimental datasets to systematically identify and analyze NNIs. The current version catalogs over 90,000 interactions spanning eight categories of sRNA-to-longer ncRNAs, each extensively annotated with interaction types, identification methods, and functional descriptions. The integrated schema and advanced visualization framework in ANNInter enable users to explore intricate interaction networks, providing system-wide insights into ncRNA-mediated regulation. These interaction data provide unparalleled opportunities to uncover the regulatory roles of NNIs in key biological processes such as growth regulation, stress adaptation, and cellular signaling. By providing an extensive, curated repository of computational and degradome-based interaction data, ANNInter will provide a platform to the study of ncRNA biology, elucidating the complex mechanisms of NNIs and supporting the concept of competing endogenous RNAs (ceRNAs) in gene regulation. The platform is freely accessible at https://www.nipgr.ac.in/ANNInter/.
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    The landscape of fusion transcripts in plants: a new insight into genome complexity
    (BioMed Central Ltd, 2024) Chitkara, Pragya; Singh, Ajeet; Gangwar, Rashmi; Bhardwaj, Rohan; Zahra, Shafaque; Arora, Simran; Hamid, Fiza; Arya, Ajay; Sahu, Namrata; Chakraborty, Srija; Ramesh, Madhulika; Kumar, Shailesh
    Background Fusion transcripts (FTs), generated by the fusion of genes at the DNA level or RNA-level splicing events significantly contribute to transcriptome diversity. FTs are usually considered unique features of neoplasia and serve as biomarkers and therapeutic targets for multiple cancers. The latest findings show the presence of FTs in normal human physiology. Several discrete reports mentioned the presence of fusion transcripts in planta, has important roles in stress responses, morphological alterations, or traits (e.g. seed size, etc.). Results In this study, we identified 169,197 fusion transcripts in 2795 transcriptome datasets of Arabidopsis thaliana, Cicer arietinum, and Oryza sativa by using a combination of tools, and confirmed the translational activity of 150 fusion transcripts through proteomic datasets. Analysis of the FT junction sequences and their association with epigenetic factors, as revealed by ChIP-Seq datasets, demonstrated an organised process of fusion formation at the DNA level. We investigated the possible impact of three-dimensional chromatin conformation on intra-chromosomal fusion events by leveraging the Hi-C datasets with the incidence of fusion transcripts. We further utilised the longread RNA-Seq datasets to validate the most reoccurring fusion transcripts in each plant species followed by further authentication through RT-PCR and Sanger sequencing. Conclusions Our findings suggest that a significant portion of fusion events may be attributed to alternative splicing during transcription, accounting for numerous fusion events without a proportional increase in the number of RNA pairs. Even non-nuclear DNA transcripts from mitochondria and chloroplasts can participate in intra- and inter-chromosomal fusion formation. Genes in close spatial proximity are more prone to undergoing fusion formation, especially in intra-chromosomal FTs. Most of the fusion transcripts may not undergo translation and serve as long non-coding RNAs. The low validation rate of FTs in plants indicated that the fusion transcripts are expressed at very low levels, like in the case of humans. FTs often originate from parental genes involved in essential biological processes, suggesting their relevance across diverse tissues and stress conditions. This study presents a comprehensive repository of fusion transcripts, offering valuable insights into their roles in vital physiological processes and stress responses.