Browsing by Author "Vivek, A. T."

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    AlnC: An extensive database of long non-coding RNAs in angiosperms
    (PLOS, 2021) Singh, Ajeet; Vivek, A. T.; Kumar, Shailesh
    Long non-coding RNAs (lncRNAs) are defined as transcripts of greater than 200 nucleotides that play a crucial role in various cellular processes such as the development, differentiation and gene regulation across all eukaryotes, including plant cells. Since the last decade, there has been a significant rise in our understanding of lncRNA molecular functions in plants, resulting in an exponential increase in lncRNA transcripts, while these went unannounced from the major Angiosperm plant species despite the availability of large-scale high throughput sequencing data in public repositories. We, therefore, developed a user-friendly, openaccess web interface, AlnC (Angiosperm lncRNA Catalogue) for the exploration of lncRNAs in diverse Angiosperm plant species using recent 1000 plant (1KP) trancriptomes data. The current version of AlnC offers 10,855,598 annotated lncRNA transcripts across 682 Angiosperm plant species encompassing 809 tissues. To improve the user interface, we added features for browsing, searching, and downloading lncRNA data, interactive graphs, and an online BLAST service. Additionally, each lncRNA record is annotated with possible small open reading frames (sORFs) to facilitate the study of peptides encoded within lncRNAs. With this user-friendly interface, we anticipate that AlnC will provide a rich source of lncRNAs for small-and large-scale studies in a variety of flowering plants, as well as aid in the improvement of key characteristics in relevance to their economic importance. Database URL: http://www.nipgr.ac.in/AlnC
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    Identification of virus-derived small interfering RNAs (vsiRNAs) from infected sRNA-Seq samples
    (Springer Nature Publishing AG, 2024) Vivek, A. T.; Kumar, Shailesh
    Plants have developed sophisticated defense mechanisms to combat viral infections, prominently utilizing Dicer-like enzymes (DCL) for generating virus-derived small interfering RNAs (vsiRNAs) through RNA interference (RNAi). This intrinsic mechanism effectively impedes virus replication. Exploiting their potential, vsiRNAs have become a major focus area for comprehensive viral investigations in plants, integrating both bioinformatics and experimental strategies. This chapter introduces an up-to-date computational workflow optimized for identifying and comprehensively annotating vsiRNAs with the utilization of small RNA sequencing (sRNA-seq) data collected from virus-infected plants. The workflow detailed in this chapter centers on known plant-targeting viruses, providing step-by-step guidance to enhance vsiRNA analysis, ultimately advancing the comprehension of plant-virus interactions.