Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes

• Published in: Virology (New York, N.Y.) N.Y.), 2009-09, Vol.392 (2), p.203-214
• Main Authors: Donaire, Livia, Wang, Yu, Gonzalez-Ibeas, Daniel, Mayer, Klaus F, Aranda, Miguel A, Llave, César
• Format: Article
• Language: English
• Subjects: Antisense; Arabidopsis thaliana; Base Sequence; Census; Chromatin; Cucumber mosaic virus; Cucumis melo; Cymbidium ringspot virus; Data processing; Double-stranded RNA; Enzymes; Genome, Viral; Genomes; genomics; host-pathogen relationships; Hot spots; Infection; Infectious Disease; Melon necrotic spot virus; Molecular Sequence Data; Nucleic Acid Conformation; Nucleotides; Pepper mild mottle virus; Plant virus; Plant viruses; Plant Viruses - genetics; Plant–virus interactions; Potato virus X; RNA silencing; RNA Viruses - genetics; RNA, Viral - genetics; RNA-mediated interference; Sequence Analysis, RNA; Tobacco rattle virus; Tomato yellow leaf curl virus; Turnip mosaic virus; viral small RNA; Viral small RNAs; Watermelon mosaic virus
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1016/j.virol.2009.07.005

Abstract Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the data set. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to a better understanding of vsRNA biogenesis.