Annual Review of Phytopathology (2015) 53, 425-444

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Qingfa Wu, Shou-Wei Ding, Yongjiang Zhang and Shuifang Zhu (2015)
Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms
Annual Review of Phytopathology 53, 425-444
Abstract: A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
(The abstract is excluded from the Creative Commons licence and has been copied with permission by the publisher.)
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molecular biology - genes

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