Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses

Institute of Animal and Plant Quarantine, Chinese Academy of Inspection and Quarantine, No. 241 Huixinli, Huixin West Street, Beijing 100029, China.
Journal of virological methods (Impact Factor: 1.78). 03/2010; 167(1):53-60. DOI: 10.1016/j.jviromet.2010.03.010
Source: PubMed


A major challenge facing agriculture at present is the development of techniques that can screen field samples and other plant materials simultaneously for the presence of many viruses. Microarray techniques show promise in this regard, as their high throughput nature can potentially detect a range of viruses using a single test. In this paper we present an array that can detect a wide spectrum of 169 plant virus species from 13 different genera. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viruses at the genus level. The designed arrays showed a high specificity and sensitivity when tested with a set of standard virus samples. Field samples collected from a severe disease outbreak of Panax notoginseng farms in Yunnan, China, in 2001 were screened, where a potyvirus infection was identified associated with the disease.

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    • "Engel et al. (2010) constructed a microarray system containing 570 unique viral oligonucleotides designed to detect 44 different grapevine viruses. Zhang et al. (2010) presented an array to detect a wide spectrum of 169 plant virus species from 13 different genera. Abdullahi et al. (2011) designed the microarray system for detection of 15 virus species infecting grapevine with 162 oligonucleotide probes. "
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    ABSTRACT: A large-scale oligonucleotide (LSON) chip was developed for the detection of the plant viruses with known genetic information. The LSON chip contains two sets of 3,978 probes for 538 species of targets including plant viruses, satellite RNAs and viroids. A hundred forty thousand probes, consisting of isolate-, species- and genus-specific probes respectively, are designed from 20,000 of independent nucleotide sequence of plant viruses. Based on the economic importance, the amount of genome information, and the number of strains and/or isolates, one to fifty-one probes for each target virus are selected and spotted on the chip. The standard and field samples for the analysis of the LSON chip have been prepared and tested by RT-PCR. The probe's specific and/or nonspecific reaction patterns by LSON chip allow us to diagnose the unidentified viruses. Thus, the LSON chip in this study could be highly useful for the detection of unexpected plant viruses, the monitoring of emerging viruses and the fluctuation of the population of major viruses in each plant.
    The plant pathology journal 03/2014; 30(1). DOI:10.5423/PPJ.OA.08.2013.0084 · 0.72 Impact Factor
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    • "After a series of elution process, sequences of failed hybridization are washed off, and the successful hybridization duplex complexes can be observed by a fluorescent signal. Because of its simple operation, and high levels of repeatability and accuracy, microarray technology has been applied to species identification, for example in the detection of pathogenic microorganisms (Korimbocus et al. 2005; Garaizar et al. 2006; Zhang et al. 2010). Furthermore, numerous COI probes have been designed and used for species identification in the animal kingdom. "
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    ABSTRACT: Rapid and accurate identification of species is required for the biological control of pest Noctuoidea moths. DNA barcodes and thin-film biosensor chips are two molecular approaches that have gained wide attention. Here, we compare these two methods for the identification of a limited number of Noctuoidea moth species. Based on the commonly used mitochondrial gene cytochrome c oxidase I (the standard DNA barcode for animal species), 14 probes were designed and synthesized for 14 species shared by two national nature reserves in Beijing and Hebei, China. Probes ranged in length from 18 to 27 bp and were designed as mismatch probes to guarantee that there were at least three base differences between the probe and nontarget sequences. The results on the chip could be detected by the naked eye without needing special equipment. No cross-hybridizations were detected although we tested all probes on the 14 target and 24 nontarget Noctuoidea species. The neighbour-joining tree of the 38 species based on COI sequences gave 38 highly supported independent groups. Both DNA barcoding and thin-film biosensor chips, based on the COI gene, are able to accurately identify and discriminate the 14 targeted moth species in this study. Because of its speed, high accuracy and low cost, the thin-film biosensor chip is a very practical means of species identification. Now, a more comprehensive chip will be developed for the identification of additional Noctuoidea moths for pest control and ecological protection.
    Molecular Ecology Resources 08/2013; 14(1). DOI:10.1111/1755-0998.12165 · 3.71 Impact Factor
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    • "The power of multiplexing in microarrays has been amply demonstrated for a variety of animal viruses (Chizhikov et al., 2002; Erlandsson et al., 2011; Klaassen et al., 2004; Kozal et al., 1996; Wang et al., 2002). In plants, the initial adoption of microarrays for virus detection began at a slower pace with a limited number of virus targets (Boonham et al., 2003; Bystricka et al., 2005; Grover et al., 2010; Pasquini et al., 2008; Wei et al., 2009), although recent reports demonstrate a much broader applicability (Tiberini et al., 2010; Zhang et al., 2010) with collections of probes designed to detect up to 52 or more virus species (Bagewadi et al., 2010; Nicolaisen, 2011). The other benefit of an array system is the theoretical increase in the breadth of detection inherent in the hybridization kinetics (Naiser et al., 2008; Peterson et al., 2002) between the probe and its target; allowing complementary interactions to occur even when minor mismatches are present (Grover et al., 2010). "
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    ABSTRACT: Grapevine leafroll-associated viruses (GLRaVs) are an emerging group of viruses that represent a significant threat to the global productivity and sustainability of the grapevine industry. Their control is achieved through the identification and elimination of infected vines, and the use of planting material derived from virus-tested, certified stocks. As such, much effort has been invested in developing reliable molecular diagnostic techniques. In this work, we report the development of a macroarray assay for the detection of the principal GLRaVs. In total 314 70-mer oligonucleotides specific to GLRaV-1, -2, -3, -4, -7, and GLRaV-4 strains 5, 6, 9 and Pr were spotted onto a 11×7cm nylon membrane. Thirty-four grapevine samples from various origins were tested by the macroarray, RT-PCR and ELISA. Thirty were positive for virus infection using RT-PCR, 28 by ELISA and 25 by the macroarray. Mixed infections were identified by macroarray in two samples and confirmed by RT-PCR or ELISA. There were a few discrepancies between methods that were most likely due to differences in the sensitivity of detection, and in the case of the macroarray, limitations in the sequence data available for certain virus species in the design of the oligonucleotides. This work demonstrates the successful application of macroarray methodology using randomly primed and sequence-nonspecific amplified cDNAs derived from grapevine total RNA extracts, and provides a proof-of-principal for unbiased multiplex detection using a single robust platform.
    Journal of virological methods 05/2012; 183(2):161-9. DOI:10.1016/j.jviromet.2012.04.008 · 1.78 Impact Factor
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