Browsing by Author "Vivek, A.T."

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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.
athisomiRDB: A comprehensive database of Arabidopsis isomiRs
(Oxford University Press, 2024) Vivek, A.T.; Arya, Ajay; Swain, Supriya P.; Kumar, Shailesh
Several pieces of evidence challenge the traditional view of miRNAs as static molecules, revealing dynamic isomiRs originating from each miRNA precursor arm. In plants, isomiRs, which result from imprecise cleavage during pre-miRNA processing and post-transcriptional alterations, serve as crucial regulators of target microRNAs (miRNAs). Despite numerous studies on Arabidopsis miRNAs, the systematic identification and annotation of isomiRs across various tissues and conditions remain limited. Due to the lack of systematically collected isomiR information, we introduce the athisomiRDB database, which houses 20 764 isomiRs from Arabidopsis small RNA-sequencing (sRNA-seq) libraries. It comprises >2700 diverse samples and allows exploration at the sample, miRNA, or isomiR levels, offering insights into the presence or absence of isomiRs. The athisomiRDB includes exclusive and ambiguous isomiRs, each with features such as transcriptional origin, variant-containing isomiRs, and identifiers for frequent single-nucleotide polymorphisms from the 1001 Genomes Project. It also provides 3ʹ nontemplated post-transcriptional additions, isomiR–target interactions, and trait associations for each isomiR. We anticipate that athisomiRDB will play a pivotal role in unraveling the regulatory nature of the Arabidopsis miRNAome and enhancing sRNA research by leveraging isomiR profiles from extensive sRNA-seq datasets. Database URL: https://www.nipgr.ac.in/athisomiRDB
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
(Oxford University Press, 2021) Vivek, A.T.; Kumar, Shailesh
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants
(Elsevier B.V., 2020) Vivek, A.T.; Zahra, Shafaque; Kumar, Shailesh
Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.