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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #306869

Research Project: Characterization, Etiology, and Disease Management for Vegetable Crops

Location: Vegetable Research

Title: Using small RNA (sRNA) deep sequencing to understand global virus distribution in plants

Author
item Padmanabhan, Chellappan
item Gao, Shan - Boyce Thompson Institute
item Li, Rugang
item Fei, Zhangjun - Boyce Thompson Institute
item Ling, Kai-shu

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/14/2014
Publication Date: 10/19/2014
Citation: Padmanabhan, C., Gao, S., Li, R., Fei, Z., Ling, K. 2014. Using small RNA (sRNA) deep sequencing to understand global virus distribution in plants. Cell Symposia-Regulatory RNAs. Meeting Abstract. P. 22.

Interpretive Summary: N/A

Technical Abstract: Small RNAs (sRNAs), a class of regulatory RNAs, have been used to serve as the specificity determinants of suppressing gene expression in plants and animals. Next generation sequencing (NGS) uncovered the sRNA landscape in most organisms including their associated microbes. In the current study, we took advantage of the NGS technology as a platform to uncover a comprehensive virus composition in tomato samples suspicious of viral infection from multiple locations around the world. Over 142 sRNA libraries were constructed and sequenced on Illumina HiSeq 2000. After in-silico subtraction of ~90% host sRNAs, the virus-like exogenous sRNAs were assembled with or without reference virus or viroid genomes. Interestingly, we were able to retrieve a total of 2,171 viruses including ~182 of near complete viral genomes and ~1,836 partial viral genomes assembled with reference virus genome. Most importantly, approximately ~153 novel viral genomes were assembled with less than 60% nucleotide sequence identity to the existing viral genomes in the current NCBI databases. Furthermore, as a measure in validation of the assembled viral genome sequences, we randomly selected four libraries and identified six viruses through Sanger sequencing, which in fact matched very well with the assembled viral genome sequences generated from deeply sequenced sRNAs. In addition to tomato, this approach has been successfully applied for virus identification on 21 other plant species. Therefore, deep sequencing using NGS and assembly of sRNAs provides a great advantage for accurate identification of causal agents of viral diseases with either known or unknown sequences.