alexa A Case Study on Discovery of Novel Citrus Leprosis Virus Cytoplasmic Type 2 Utilizing Small RNA Libraries by Next Generation Sequencing and Bioinformatic Analyses
ISSN: 2153-0602

Journal of Data Mining in Genomics & Proteomics
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Review Article

A Case Study on Discovery of Novel Citrus Leprosis Virus Cytoplasmic Type 2 Utilizing Small RNA Libraries by Next Generation Sequencing and Bioinformatic Analyses

Avijit Roy1,3*,#, Jonathan Shao2#, John S Hartung2, William Schneider3 and RH Brlansky1

1University of Florida, IFAS, Plant Pathology Department, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred, FL, USA

2USDA-ARS, MPPL, Beltsville, MD, USA

3USDA-ARS, FDWSRU, Ft. Detrick, MD, USA

#Avijit Roy and Jonathan Shao should be considered as co-first authors.

*Corresponding Author:
Avijit Roy
University of Florida
Citrus Research and Education Center
700, Experiment Station Road
Lake Alfred, Florida 33850, USA
Tel: +1-863-956-8703
Fax: +1-863-956-4631
E-mail: [email protected]

Received date: May 09, 2013; Accepted date: May 28, 2013; Published date: June 05, 2013

Citation: Roy A, Shao J, Hartung JS, Schneider W, Brlansky RH (2013) A Case Study on Discovery of Novel Citrus Leprosis Virus Cytoplasmic Type 2 Utilizing Small RNA Libraries by Next Generation Sequencing and Bioinformatic Analyses. J Data Mining Genomics Proteomics 4:129. doi:10.4172/2153-0602.1000129

Copyright: © 2013 Roy A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source and source are credited.

 

Abstract

The advent of innovative sequencing technology referred to as “Next-Generation” Sequencing (NGS), provides a new approach to identify the ‘unknown known’ and ‘unknown unknown’ viral pathogens without a priori knowledge. The genomes of plant viruses can be rapidly determined even when occurring at extremely low titers in the infected host. The method is based on massively parallel sequencing of the population of small RNA molecules 18-35 nucleotides in length produced by RNA silencing host defense. Improvements in chemistries, bioinformatic tools and advances in engineering has reduced the costs of NGS, increased its accessibility, and enabled its application in the field of plant virology. In this review, we discuss the utilization of the Illumina GA IIX platform combined with the application of molecular biology and bioinformatic tools for the discovery of a novel cytoplasmic Citrus leprosis virus (CiLV). This new virus produced symptoms typical of CiLV but was not detected with either serological or PCR-based assays for the previously described virus. The new viral genome was also present in low titer in sweet orange (Citrus sinensis), an important horticultural crop with incomplete genomic resources. This is a common situation in horticultural research and provides an example of the broader utility of this approach. In addition to the discovery of novel viruses, the sequence data may be useful for studies of viral evolution and ecology and the interactions between viral and host transcriptomes.

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