High-throughput Sequencing Reveals vsiRNAs Derived from Cucumber green mottle mosaic virus-infected Watermelon

Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, and is a serious pathogen of Cucurbitaceae crops. Virus-derived small interfering RNAs (vsiRNAs), which are processed by Dicer-like and Argonaute proteins as well as RNA-dependent RNA polymerase, mediate the silencing of viral genomic RNA and host transcripts. To identify the CGMMV derived vsiRNAs and reveal interactions between CGMMV and watermelon host plant, deep sequencing technology was used to identify and characterize the vsiRNAs derived from CGMMV in infected watermelon plants in present study. A total of 10 801 368 vsiRNA reads representing 71 583 unique sRNAs were predicted in CGMMV-inoculated watermelon plants. The CGMMV vsiRNAs were mostly 21 or 22 nt long. The majority of the CGMMV vsiRNAs (i.e., 91.7%) originated from the viral sense strand. Additionally, uracil was the predominant 5′-terminal base of vsiRNAs. Furthermore, the putative targets and functions of some of the CGMMV vsiRNAs were predicted and investigated. The results enhance our understanding of the interaction between CGMMV and the host watermelon and provide molecular basis for CGMMV resistance improvement in watermelon and other Cucurbitaceae crops.