Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids

Tiberini, Antonio; Barba, M.

doi:10.1016/j.jviromet.2012.05.028

Cited by 23 publications

(9 citation statements)

References 34 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sensitivity and specificity can be improved controlling the hybridization temperature and buffer composition (Boonham et al, 2007). Microarrays have been used to detect: i) viruses infecting a particular crop, such as tomato, cucurbits, potato and grapevine (Bystricka et al, 2003;Engel et al, 2010;Sip et al, 2010;Tiberini et al, 2010;Tiberini and Barba, 2012); ii) different viral species of a genus (Wei et al, 2009); and iii) isolates or variants of the same virus (Deyong et al, 2005;Pasquini et al, 2008). Microarrays have been improved to detect hundreds of plant viruses, including genus-specific oligoprobes (Zhang et al, 2010;Nicolaisen, 2011;Nam et al, 2014).…”

Section: Multiplexingmentioning

confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

View full text Add to dashboard Cite

Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.

show abstract

Section: Multiplexingmentioning

confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

View full text Add to dashboard Cite

show abstract

“…Previously, only a few microarrays were reported to detect a subset of plant viroids. A recently published microarray was able to detect six viroid species from the Pospiviroid genus [45]. A commercial microarray was constructed that is able to detect 7 viroid genera [47].…”

Section: Discussionmentioning

confidence: 99%

A Universal Oligonucleotide Microarray with a Minimal Number of Probes for the Detection and Identification of Viroids at the Genus Level

et al. 2013

View full text Add to dashboard Cite

A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.

show abstract

“…When designed, a DNA microarray can be used routinely as a test for the presence of various phytopathogens (Zhang et al 2010;Tiberini and Barba 2012). However, to our knowledge, none of the described DNA microarrays is suitable for the detection of microbial, maize pathogens.…”

Section: Discussionmentioning

confidence: 99%

DNA microarray-based detection and identification of bacterial and viral pathogens of maize

et al. 2017

View full text Add to dashboard Cite

We describe the construction and evaluation of DNA microarray for simultaneous detection and identification of five microbial pathogens of maize: Pantoea ananatis, P. agglomerans, Enterobacter cloaceae subsp. dissolvens, Maize dwarf mosaic virus (MDMV) and Sugarcane mosaic virus (SCMV). Unlike other DNA microarrays described, our microarray comprises probes targeting the whole genomes of the tested pathogens. Control probes are complementary to genomes of closely related microorganisms that are nonpathogenic to maize and against maize and human genome sequences in order to avoid the potential false-positive results. Obtained results indicate that the fluorescence signals from pathogen and control probes are well distinguished in all performed experiments. The microarray's performance was compared with classical PCR-based pathogen detection method, and the versatility of the assay was tested in silico.

show abstract

Optimization and improvement of oligonucleotide microarray-based detection of tomato viruses and pospiviroids

Cited by 23 publications

References 34 publications

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

A Universal Oligonucleotide Microarray with a Minimal Number of Probes for the Detection and Identification of Viroids at the Genus Level

DNA microarray-based detection and identification of bacterial and viral pathogens of maize

Contact Info

Product

Resources

About