Abstract
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.
Highlights
The emergence of high-throughput, fast and cost-effective generation sequencing (NGS) technology has facilitated the study of small non-coding ribonucleic acids (RNAs) in eukaryotes and their role in Ribonucleic acids (RNA) silencing mechanisms as a defense response during pathogen infection
virusinduced gene silencing (VIGS) assists in the process of chromatin modification, translation process and a potent mediator for gene expression regulation bestowing the overall resistance in host plants against the viral defense
A majority of these RNA molecules comprises of small interfering RNAs (siRNAs) with length ranging from 21 to 24 nucleotide with 3 unphosphorylated overhangs of 2 nt are known to be the potential regulators of gene expression as a part of a natural anti-defense system for the host plant [7]
Summary
The emergence of high-throughput, fast and cost-effective generation sequencing (NGS) technology has facilitated the study of small non-coding ribonucleic acids (RNAs) in eukaryotes and their role in RNA silencing mechanisms as a defense response during pathogen infection. VsiRNAs after assembling with RISC act in a sequence-specific manner and bind to its homologous complementary viral genomic RNA or genomic DNA transcript and thereby silencing viral expression and imparting anti-viral resistance to the host plant [8, 15]. Less explored, they are supposed to regulate cellular processes via epigenetic modifications like DNA methylation of gene promoters [16].
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