1.
Rapid Detection of Ustilaginoidea virens from Rice using Loop-Mediated Isothermal Amplification Assay.
Yang, X, Al-Attala, MN, Zhang, Y, Zhang, AF, Zang, HY, Gu, CY, Gao, TC, Chen, Y, Al-Attala, MN, Ali, F, et al
Plant disease. 2018;(9):1741-1747
Abstract
Ustilaginoidea virens is an important fungus that causes rice false smut disease. This disease significantly reduces both grain yield and quality. Various methods have been developed for the detection of U. virens but most of these methods need sophisticated equipment such as a thermal cycler. Here, we present a loop-mediated isothermal amplification (LAMP) assay for the specific detection of U. virens. This assay used a specific region of the UvG-β1 gene (212-bp region) to design six LAMP primers. The LAMP assay was optimized by the combination of rapidity, simplicity, and high sensitivity for the detection of about 1 pg of target genomic DNA in the reaction whereas, with polymerase chain reaction (PCR), there was no amplification of DNA with concentrations less than 1 ng. Among the genomic DNA of 22 fungus species and two strains of U. virens, only the tube containing the DNA of U. virens changed to yellowish green with SYBR Green I. The color change was indicative of DNA amplification. No DNA was amplified from either the other 22 fungus species or the negative control. Moreover, 20 spikelets and 22 rice seed samples were used for the detection of rice false smut via LAMP. The results were comparable with conventional PCR. We conclude that gene UvG-β1 coupled with LAMP assay, can be used for the detection and identification of U. virens gene via LAMP.
2.
Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms.
Wu, Q, Ding, SW, Zhang, Y, Zhu, S
Annual review of phytopathology. 2015;:425-44
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.
3.
The Rice stripe virus pc4 functions in movement and foliar necrosis expression in Nicotiana benthamiana.
Zhang, C, Pei, X, Wang, Z, Jia, S, Guo, S, Zhang, Y, Li, W
Virology. 2012;(2):113-21
Abstract
The Rice stripe virus (RSV) pc4 has been determined as the viral movement protein (MP). In this study, the pc4 gene was cloned into a movement-deficient Tobacco mosaic virus (TMV). The resulting hybrid TMV-pc4, in addition to spreading cell to cell in Nicotiana tabacum, moved systemically and induced foliar necrosis in Nicotiana benthamiana, indicating novel functions of the RSV MP. A systematic alanine-scanning mutagenesis study established the region K(122)-D(258) of the pc4 substantially associated with cell-to-cell movement, and mutants by replacement of KGR(122-124), D(135), ED(170-171), ER(201-202), EFE(218-220) or ELD(256-258) with alanine(s) no longer moved cell to cell. However, only one amino acid group KGR(122-124) was linked with long-distance movement. The region D(17)-K(33) was recognized as a crucial domain for leaf necrosis response, and mutagenesis of DD(17-18) or RK(32-33) greatly attenuated necrosis. The overall data suggested manifold roles of the pc4 during the RSV infection in its experimental host N. benthamiana.