In Silico Probe-Based Detection of Citrus Viruses in NGS Data

Jooste, Tracey; Visser, Marike; Cook, Glynnis; Burger, Johan T.; Maree, Hans J.

doi:10.1094/phyto-10-16-0379-r

Cited by 8 publications

(3 citation statements)

References 15 publications

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“…Analyzed siRNAs showed the pathogen regions associated with increased silencing and an altered plant hormone regulatory pattern. The same group developed and evaluated e-probes to be applied on citrus massive sequencing for rapid, simultaneous identification of 11 recognized viruses and viroids [ 95 ]. This e-probe-based approach was applied to screen different samples and RNA template, and mainly for CTV genotyping.…”

Section: Application Of High-throughput Sequencing Technology To Dmentioning

confidence: 99%

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Maliogka

Minafra

Saldarelli

et al. 2018

Viruses

105

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Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.

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Section: Application Of High-throughput Sequencing Technology To Dmentioning

confidence: 99%

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Maliogka

Minafra

Saldarelli

et al. 2018

Viruses

105

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“…Proper guidelines need to be developed before NGS can be used as a certification tool. There is an effort to integrate NGS as an important tool for certification in South Africa [26,27]. In the present study, 21 plant samples, including fifteen from the pathogen-positive inventory of the USDA National Clonal Germplasm Repository for Citrus & Dates, Riverside, California, USA, were analyzed by NGS transcriptome study.…”

Section: Introductionmentioning

confidence: 99%

Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange

Keremane,

Singh,

Ramadugu

et al. 2024

Plants

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Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the “fatal yellows” disease.

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“…This approach has been useful for the rapid and simultaneous identification of 11 recognized viruses, including CPsV. This latter has been detected in only one field sample and the result was confirmed with de novo assembly-based similarity searches and RT-PCR [ 93 ].…”

Section: Methods To Detect the Diseasementioning

confidence: 93%

Citrus Psorosis Virus: Current Insights on a Still Poorly Understood Ophiovirus

et al. 2020

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Citrus psorosis was reported for the first time in Florida in 1896 and was confirmed as a graft-transmissible disease in 1934. Citrus psorosis virus (CPsV) is the presumed causal agent of this disease. It is considered as a type species of the genus Ophiovirus, within the family Aspiviridae. CPsV genome is a negative single-stranded RNA (-ssRNA) with three segments. It has a coat protein (CP) of 48 kDa and its particles are non-enveloped with naked filamentous nucleocapsids existing as either circular open structures or collapsed pseudo-linear forms. Numerous rapid and sensitive immuno-enzymatic and molecular-based detection methods specific to CPsV are available. CPsV occurrence in key citrus growing regions across the world has been spurred the establishment of the earliest eradication and virus-free budwood programs. Despite these efforts, CPsV remains a common and serious challenge in several countries and causes a range of symptoms depending on the isolate, the cultivar, and the environment. CPsV can be transmitted mechanically to some herbaceous hosts and back to citrus. Although CPsV was confirmed to be seedborne, the seed transmission is not efficient. CPsV natural spread has been increasing based on both CPsV surveys detection and specific CPsV symptoms monitoring. However, trials to ensure its transmission by a soil-inhabiting fungus and one aphid species have been unsuccessful. Psorosis disease control is achieved using CPsV-free buds for new plantations, launching budwood certification and indexing programs, and establishing a quarantine system for the introduction of new varieties. The use of natural resistance to control CPsV is very challenging. Transgenic resistance to at least some CPsV isolates is now possible in at least some sweet orange varieties and constitutes a promising biotechnological alternative to control CPsV. This paper provides an overview of the most remarkable achievements in CPsV research that could improve the understanding of the disease and lead the development of better control strategies.

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In Silico Probe-Based Detection of Citrus Viruses in NGS Data

Cited by 8 publications

References 15 publications

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange

Citrus Psorosis Virus: Current Insights on a Still Poorly Understood Ophiovirus

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