Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay

Tan, Shih-hua; Osman, Fatima; Bodaghi, Sohrab; Dang, Tyler; Greer, Greg; Huang, Amy; Hammado, Sarah; Abu-Hajar, Shurooq; Campos, Roya; Vidalakis, Georgios

doi:10.1371/journal.pone.0223958

Cited by 18 publications

(14 citation statements)

References 51 publications

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“…Several platforms for second-generation sequencing have been developed by different companies such as Roche 454, Illumina, Solid and Ion Torrent (Bleidorn, 2016;Goodwin et al, 2016;Heather and Chain, 2016;Villamor et al, 2019). In addition to detection of new plant viruses and viroids, HTS is being used for studies on epidemiology, synergistic interactions between viruses, and genetic diversity and evolutionary mechanisms of virus populations (Kehoe et al, 2014;Hadidi et al, 2016;Pecman et al, 2017;Roossinck, 2017;Tan et al, 2019;Xu et al, 2019).…”

Section: High-throughput Sequencingmentioning

confidence: 99%

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

2020

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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.

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Section: High-throughput Sequencingmentioning

confidence: 99%

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

2020

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“…Various RNA isolation methods have been successfully used with different plant tissues for downstream detection of plant pathogens (MacKenzie et al, 1997;Portillo et al, 2006;Osman et al, 2012;Sun et al, 2014;Martinelli et al, 2015;Ali et al, 2017;Inglis et al, 2018;Liu et al, 2018;Vennapusa et al, 2020). More specifically, for citrus tissues, low-throughput phenolchloroform based methods with cetrimonium bromide (CTAB) or TRIzol ® (Thermo Fisher Scientific, Waltham, MA), and silica column-based kits such as the RNeasy ® Plant Mini Kit (Qiagen, Valencia, CA) or Spectrum ™ Plant Total RNA (Sigma-Aldrich, St. Louis, MO) have been effectively utilized for RNA isolation and detection of citrus viruses and viroids using RT-PCR and RT-qPCR assays (Li et al, 2008;Saponari et al, 2008;Damaj et al, 2009;Wang et al, 2013a;Wang et al, 2013b;Tan et al, 2019;Bester et al, 2021;Benıtez-Galeano et al, 2021). More recently, high-throughput semi-automated total nucleic acid isolation systems such as the MagMAX ™ Express-96 (Thermo Fisher Scientific, Waltham, MA) and BioSprint ® 96 (Qiagen, Valencia, CA), capable of isolating RNA from up to 96 samples at once, have been used successfully in citrus pathogen detection protocols including but not limited to viruses and viroids (Osman et al, 2015;Osman et al, 2017;Braswell et al, 2020;Dang et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of RNA isolation methods optimized for high-throughput detection of viral pathogens in California’s regulatory and disease management program for citrus propagative materials

Dang

Bodaghi²,

Osman³

et al. 2022

Front. Agron.

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Citrus germplasm programs can benefit from high-throughput polymerase chain reaction (PCR)-based methods for the detection of graft-transmissible pathogens in propagative materials. These methods increase diagnostic capacity, and thus contribute to the prevention of disease spread from nurseries to citrus orchards. High quality nucleic acids, as determined by purity, concentration, and integrity, are a prerequisite for reliable PCR detection of citrus pathogens. Citrus tissues contain high levels of polyphenols and polysaccharides, which can affect nucleic acid quality and inhibit PCR reactions. Various commercially available RNA isolation methods are used for citrus and include: phenol-chloroform (TRIzol®, Thermo Fisher Scientific); silica columns (RNeasy® Plant Mini Kit, Qiagen); and magnetic beads-based methods (MagMAX™-96 Viral RNA Isolation Kit, Thermo Fisher Scientific). To determine the quality of RNA and its impact on the detection of graft-transmissible citrus pathogens in reverse transcription (RT) PCR-based assays, we compared these three RNA isolation methods. We assessed RNA purity, concentration, and integrity from citrus inoculated with different viruses and viroids. All three RNA isolation methods produced high quality RNA, and its use in different RT-PCR assays resulted in the detection of all targeted citrus viruses and viroids with no false positive or negative results. TRIzol® yielded RNA with the highest concentration and integrity values but some samples required serial dilutions to remove PCR inhibitors and detect the targeted pathogens. The RNeasy® kit produced the second highest concentration and purity of RNA, and similar integrity to TRIzol®. MagMAX™ isolation also provided high quality RNA but most importantly produced RNA with consistent results clustered around a median value for concentration, purity, and integrity. Subsequently, MagMAX™-96 was combined with the semi-automated MagMAX™ Express-96 Deep Well Magnetic Particle Processor, for high-throughput sample processing. MagMAX™-96 enabled the diagnostic laboratory of the Citrus Clonal Protection Program-National Clean Plant Network at the University of California, Riverside to process over 16,500 samples from citrus budwood source trees between 2010 and 2019. This high-throughput approach dramatically reduced the incidence of viroids in citrus nurseries and was key to the successful implementation of the mandatory Citrus Nursery Stock Pest Cleanliness Program in California.

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“…Over the last decade, an unprecedented number of viruses have been discovered using high-throughput sequencing (HTS), which led to the advancement of our knowledge on viral diversity in nature, particularly apprehending and deciphering the virome of many crops [ 89 ]. This approach has been often applied to study and identify new viruses in fruit tree species, including citrus [ 90 , 91 , 92 ]. The electronic-probe (e-probe) bioinformatics approach has been developed and evaluated recently for its ability to detect several citrus viruses simultaneously in HTS data.…”

Section: Methods To Detect the Diseasementioning

confidence: 99%

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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Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay

Cited by 18 publications

References 51 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 comparative analysis of RNA isolation methods optimized for high-throughput detection of viral pathogens in California’s regulatory and disease management program for citrus propagative materials

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

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