Abstract

RNA silencing (RS) is a conserved mechanism in a broad range of eukaryotes. In plants, RSacts as an antiviral system and a successful virus infection requires suppression or evasion of theinduced silencing response. Small interfering RNAs (siRNAs) accumulate in plants infected withRNA and DNA viruses and provide specificity to this RNA mediated immune system.High-throughput sequencing has contributed to expanding our knowledge of siRNApopulations better describing their abundance, complexity and diversity in infected tissues. VirusderivedsiRNAs (vsiRNAs, 21-24 nt) from virus-infected plants are extraordinarily abundant anddiverse. However, certain regions of viral genomes ("hot spots") are usually more represented thanothers in sequenced vsiRNA populations.Potato virus Y (PVY) is an important pathogen of solanaceous crops belonging to the largestplant virus family, Potyviridae. The PVY genome is a single-stranded, positive-sense RNA of about10 kb. PVYC-to and PVY-SON41 are two PVY isolates that induce different disease symptoms ontomato (Solanum lycopersicum): while the former provokes severe leaf distortion, the latterproduces in the same host no visible phenotype.This study propose an innovative in silico approach, which consisted in mining genomicregions of PVY isolates and looking at possible PVY vsiRNAs putatively able, by sequencecomplementarity, to targeting and suppressing accumulation of host messenger RNA (mRNA) aspredicted by RS mechanisms, leading to dysfunctional biological processes that could explainisolate-specific disease phenotypes.A computational pipeline was implemented, which allowed the retrieval within the viralgenome of 21-nt vsiRNAs from PVYC-to and PVY-SON41 isolates complementary to tomatopredicted mRNA sequences (database Solgenomics, release ITAG2.3). The pipeline was based onfive bioinformatic algorithms and a relational database (DBMS MySQL) for management of theresults obtained in each steps. The comparative study for identifying the putative tomato targetgenes was performed with NCBI blast+ package 2.2 (option -task 'blastn-short' identity > 94%,max 2 mismatch or gap, alignment length > 19 bp). RandFold was employed for searching in thePVY genomes secondary structures containing putative vsiRNAs identified in previous steps. Withthis tool, five regions in the viral genome showing potential tRNA-like or microRNA-likesecondary structures were identified, that might account for as many "hot spots" of vsiRNAsaccumulation.

Autore Pugliese

• Finetti Sialer Mariella Matilde , Catalano Domenico , Cillo Fabrizio

Tutti gli autori

• Finetti-Sialer M.M.; Catalano D.; Pati I.; Cillo F.

Titolo volume/Rivista

Non Disponibile

Anno di pubblicazione

2012

ISSN

Non Disponibile

ISBN

Non Disponibile

Numero di citazioni Wos

Nessuna citazione

Ultimo Aggiornamento Citazioni

Non Disponibile

Numero di citazioni Scopus

Non Disponibile

Ultimo Aggiornamento Citazioni

Non Disponibile

Settori ERC

Non Disponibile

Codici ASJC

Non Disponibile