PAmiRDB: A web resource for plant miRNAs targeting viruses. 2019

Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
Translational Bioinformatics Group, International Centre For Genetic Engineering and Biotechnology, New Delhi, 110067, India.

MicroRNAs (miRNAs) have emerged to be essential constituents of host antiviral-defense mechanisms. The miRNA mediated antiviral mechanism was first experimentally established in animals, which proved that host miRNAs regulate viral gene expression by targeting the animal virus mRNAs. There are comparatively fewer reports about such interactions in plants, however, artificial miRNA studies prove that miRNAs play similar antiviral role in plants too. To explore the extent of this phenomenon in plant genomes, and in the absence of any publicly available resource for prediction of plant miRNAs targeting viruses, we were motivated to predict such interactions of plant miRNAs and viral genes. The intriguing results of the predictions are compiled as a database, which we have named as PAmiRDB. The current version of PAmiRDB includes more than 2600 plant miRNAs and their specific interactions with corresponding targets in approximately 500 viral species (predominantly from the major plant-infecting virus families of geminiviruses and potyviruses). PAmiRDB is a database of known plant miRNAs and their predicted targets in virus genomes. The innovative database query-interface enables global and comprehensive investigation of such predicted interactions between host miRNAs and viral genes. The database integrated-tools also helps researchers to design experiments to confirm such interactions. PAmiRDB is available at http://bioinfo.icgeb.res.in/pamirdb.

UI MeSH Term Description Entries
D010942 Plant Viruses Viruses parasitic on plants. Phytophagineae,Plant Virus,Virus, Plant,Viruses, Plant
D010944 Plants Multicellular, eukaryotic life forms of kingdom Plantae. Plants acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations. It is a non-taxonomical term most often referring to LAND PLANTS. In broad sense it includes RHODOPHYTA and GLAUCOPHYTA along with VIRIDIPLANTAE. Plant
D012333 RNA, Messenger RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm. Messenger RNA,Messenger RNA, Polyadenylated,Poly(A) Tail,Poly(A)+ RNA,Poly(A)+ mRNA,RNA, Messenger, Polyadenylated,RNA, Polyadenylated,mRNA,mRNA, Non-Polyadenylated,mRNA, Polyadenylated,Non-Polyadenylated mRNA,Poly(A) RNA,Polyadenylated mRNA,Non Polyadenylated mRNA,Polyadenylated Messenger RNA,Polyadenylated RNA,RNA, Polyadenylated Messenger,mRNA, Non Polyadenylated
D016679 Genome, Viral The complete genetic complement contained in a DNA or RNA molecule in a virus. Viral Genome,Genomes, Viral,Viral Genomes
D017791 Geminiviridae A family of plant viruses where the VIRION possesses an unusual morphology consisting of a pair of isometric particles. Transmission occurs via leafhoppers or whitefly. Some viruses cause economically important diseases in cultivated plants. There are four genera: Mastrevirus, Curtovirus, Topocuvirus, and BEGOMOVIRUS. Curtovirus,Geminivirus,Mastrevirus,Topocuvirus,Curtoviruses,Geminiviruses,Mastreviruses,Topocuviruses
D054884 Host-Pathogen Interactions The interactions between a host and a pathogen, usually resulting in disease. Host Pathogen Interaction,Host-Pathogen Relations,Pathogen-Host Interaction,Pathogen-Host Interactions,Host Pathogen Interactions,Host Pathogen Relations,Host-Pathogen Interaction,Host-Pathogen Relation,Interaction, Host Pathogen,Interaction, Host-Pathogen,Interaction, Pathogen-Host,Interactions, Host Pathogen,Interactions, Host-Pathogen,Interactions, Pathogen-Host,Pathogen Host Interaction,Pathogen Host Interactions,Pathogen Interaction, Host,Pathogen Interactions, Host,Relation, Host-Pathogen,Relations, Host-Pathogen
D017800 Potyvirus A large genus of plant viruses of the family POTYVIRIDAE which infect mainly plants of the Solanaceae. Transmission is primarily by aphids in a non-persistent manner. The type species is potato virus Y. Potato Virus Y,Potato Virus Ys,Potyviruses,Virus Ys, Potato,Ys, Potato Virus
D018745 Genome, Plant The genetic complement of a plant (PLANTS) as represented in its DNA. Plant Genome,Genomes, Plant,Plant Genomes
D018749 RNA, Plant Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis. Plant RNA
D020407 Internet A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange. World Wide Web,Cyber Space,Cyberspace,Web, World Wide,Wide Web, World

Related Publications

Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
June 2022, Bio Systems,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
October 2017, Autophagy,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
July 2017, Bioinformatics (Oxford, England),
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
January 2011, Database : the journal of biological databases and curation,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
July 2018, Viruses,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
December 2013, Journal of translational medicine,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
September 2022, 3 Biotech,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
August 2011, Current protein & peptide science,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
October 2006, Nature immunology,
Deepshikha Satish, and Sunil Kumar Mukherjee, and Dinesh Gupta
July 2005, Nucleic acids research,
Copied contents to your clipboard!