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The genomic RNAs of Tomato spotted wilt orthotospovirus are differentially targeted in infected tomato (Solanum lycopersicum) with or without Sw5 gene

Cristian Olaya: Department of Plant Pathology, Washington State University

<div>Tospoviruses cause significant losses to a wide range of agronomic and horticultural crops worldwide. The type member, <em>Tomato spotted wilt orthotospovirus</em> (TSWV) causes systemic infection in tomato, whereas its infection is localized in cultivars carrying the <em>Sw5</em> resistance gene. The response to TSWV infection in tomato cultivars with or without <em>Sw5</em> was determined at the small RNA level using the Illumina HiSeq 4000 platform. Predicted reads were aligned to reference sequences using SCRAM2 software package. The TSWV genome is differentially processed among each of the three viral genomic RNAs -Large (L), Medium (M) and Small (S)- in the <em>Sw5</em>- and <em>Sw5</em>+ genotypes. In the <em>Sw5</em>+ cultivar, the L RNA had the highest number of viral-small-interfering RNAs (vsiRNAs), whereas in the <em>Sw5</em>- cultivar the number was higher in the S RNA. Among the three-viral genomic RNAs, the distribution of hotspots showed a high number of reads per millions reads of vsiRNAs of 21 and 22 nt class at the 5’ and 3’ ends of the L and the S RNAs, with less coverage in the M RNA. In the <em>Sw5</em>- cultivar, the nature of the 5’ nucleotide-end in the siRNAs varied significantly; reads with 5’-adenine-end were the most abundant in the viral infected treatment, whereas cytosine and thiamine were more abundant in the mock control. No such differences were seen in case of resistant genotype. Our results allow identification of potential viral genome targets to be used in RNAi-based control strategies.</div>