Publications of NIPGR Scientists

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Now showing 1 - 6 of 6
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    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
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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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    PlantPepDB: A manually curated plant peptide database
    (Springer Nature Publishing AG, 2020) Das, Durdam; Jaiswal, Mohini; Khan, Fatima Nazish; Ahamad, Shahzaib; Kumar, Shailesh
    Plants produce an array of peptides as part of their innate defense mechanism against pathogens. The potential use of these peptides for various therapeutic purposes is increasing per diem. In order to excel in this research, the community requires web repositories that provide reliable and accurate information about these phyto-peptides. This work is an attempt to bridge the gaps in plant-based peptide research. PlantPepDB is a manually curated database that consists of 3848 plant-derived peptides among which 2821 are experimentally validated at the protein level, 458 have experimental evidence at the transcript level, 530 are predicted and only 39 peptides are inferred from homology. Incorporation of physicochemical properties and tertiary structure into PlantPepDB will help the users to study the therapeutic potential of a peptide, thus, debuts as a powerful resource for therapeutic research. Different options like Simple, Advanced, PhysicoChem and AA composition search along with browsing utilities are provided in the database for the users to execute dynamic search and retrieve the desired data. Interestingly, many peptides that were considered to possess only a single property were found to exhibit multiple properties after careful curation and merging the duplicate data that was collected from published literature and already available databases. Overall, PlantPepDB is the first database comprising detailed analysis and comprehensive information of phyto-peptides from a broad functional range which will be useful for peptide-based applied research. PlantPepDB is freely available at http://www.nipgr.ac.in/PlantPepDB/.
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    PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs
    (Oxford University Press, 2018) Gupta, Nikita; Zahra, Shafaque; Singh, Ajeet; Kumar, Shailesh
    Ribonucleic acids (RNA) interference mechanism has been proved to be an important regulator of both transcriptional and post-transcription controls of gene expression during biotic and abiotic stresses in plants. Virus-derived small interfering RNAs (vsiRNAs) are established components of the RNA silencing mechanism for incurring anti-viral resistance in plants. Some databases like siRNAdb, HIVsirDB and VIRsiRNAdb are available online pertaining to siRNAs as well as vsiRNAs generated during viral infection in humans; however, currently there is a lack of repository for plant exclusive vsiRNAs. We have developed ‘PVsiRNAdb (http://www.nipgr.res.in/PVsiRNAdb)’, a manually curated plant-exclusive database harboring information related to vsiRNAs found in different virus-infected plants collected by exhaustive data mining of published literature so far. This database contains a total of 322 214 entries and 282 549 unique sequences of vsiRNAs. In PVsiRNAdb, detailed and comprehensive information is available for each vsiRNA sequence. Apart from the core information consisting of plant, tissue, virus name and vsiRNA sequence, additional information of each vsiRNAs (map position, length, coordinates, strand information and predicted structure) may be of high utility to the user. Different types of search and browse modules with three different tools namely BLAST, Smith–Waterman Align and Mapping are provided at PVsiRNAdb. Thus, this database being one of its kind will surely be of much use to molecular biologists for exploring the complex viral genetics and genomics, viral–host interactions and beneficial to the scientific community and can prove to be very advantageous in the field of agriculture for producing viral resistance transgenic crops. Database URL: http://www.nipgr.res.in/PVsiRNAdb
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    PtRFdb: a database for plant transfer RNA-derived fragments
    (Oxford University Press, 2018) Gupta, Nikita; Singh, Ajeet; Zahra, Shafaque; Kumar, Shailesh
    Transfer RNA-derived fragments (tRFs) represent a novel class of small RNAs (sRNAs) generated through endonucleolytic cleavage of both mature and precursor transfer RNAs (tRNAs). These 14–28 nt length tRFs that have been extensively studied in animal kingdom are to be explored in plants. In this study, we introduce a database of plant tRFs named PtRFdb (www.nipgr.res.in/PtRFdb), for the scientific community. We analyzed a total of 1344 sRNA sequencing datasets of 10 different plant species and identified a total of 5607 unique tRFs (758 tRF-1, 2269 tRF-3 and 2580 tRF-5), represented by 487 765 entries. In PtRFdb, detailed and comprehensive information is available for each tRF entry. Apart from the core information consisting of the tRF type, anticodon, source organism, tissue, sequence and the genomic location; additional information like PubMed identifier (PMID), Sample accession number (GSM), sequence length and frequency relevant to the tRFs may be of high utility to the user. Two different types of search modules (Basic Search and Advanced Search), sequence similarity search (by BLAST) and Browse option with data download facility for each search is provided in this database. We believe that PtRFdb is a unique database of its kind and it will be beneficial in the validation and further characterization of plant tRFs. Database URL: http://www.nipgr.res.in/PtRFdb/
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    Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database
    (Oxford University Press, 2015) Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Pandey, Garima; Khan, Yusuf; Prasad, Manoj
    Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.