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Title: Deep Sequencing of Small RNAs for Virus and Viroid Identification in Tomatoes

Author
item Ling, Kai-Shu
item FEI, ZHANGJUM - Boyce Thompson Institute
item Wechter, William - Pat
item HERNAMDEZ, ALVARO - University Of Illinois

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 5/2/2011
Publication Date: 6/1/2011
Citation: Ling, K., Fei, Z., Wechter, W.P., Hernamdez, A.G. 2011. Deep Sequencing of Small RNAs for Virus and Viroid Identification in Tomatoes. Phytopathology. 101:S106.

Interpretive Summary: N/A

Technical Abstract: Viroids are the smallest (246-401 nt) self-replicating plant pathogens. Recent evidence has led to the emerging view that RNA silencing has a crucial role in viroid pathogenesis and evolution, but the small RNA (sRNA) upon viroid infection on tomato plants has not been thoroughly analyzed. The objective of the present study was to conduct deep sequencing of sRNAs in tomato and to compare the sRNA profiles upon infection by Pepino mosaic virus (PepMV) and three pospiviroids, Potato spindle tuber viroid (PSTVd), Tomato chlorotic dwarf viroid (TCDVd), and Mexican papita viroid (MPVd). sRNA libraries were prepared and sequenced using Illumina technology. Libraries were generated from four samples suspected to be infected by PSTVd, TCDVd, MPVd or PepMV. Sequencing produced from 4.8 to 6.7 million reads per library. In all four libraries, sRNAs 23 nt and 24 nt in length were most abundant, followed by 21 nt and 22 nt. Nearly 90% of the sRNA reads in each sample could be aligned to the tomato genome. The reads that did not align to the tomato genome were assembled using previously characterized PepMV and viroid genomes as scaffolds. Results showed that virus or viroid-derived sRNAs from tomato were enriched and extended over respective virus or viroid genome. Greater genetic diversity of these pathogens in field samples was also unveiled. The success of the deep-sequencing of sRNA lends itself not only to virus discovery, but also to identification of unknown viroids.