Detection of avocado sunblotch viroid variants using fluorescent single-strand conformation polymorphism analysis

Global transcriptomic analysis in avocado nursery trees reveals differential gene expression during asymptomatic infection by avocado sunblotch viroid (ASBVd)

Avocado sunblotch viroid (ASBVd) is the type species of the family Avsunviroidae and the causal agent of avocado sunblotch disease. The disease is characterised by the presence of chlorotic lesions on avocado fruit, leaves and/or stems. Infected trees may remain without chlorosis for extended periods of time, though distorted growth and reduced yield has been observed in these cases. The molecular effects of ASBVd on avocado, and members of the Avsunviroidae on their respective hosts in general, remain poorly understood. Host global transcriptomic studies within the family Pospiviroidae have identified several host pathways that are affected during these plant-pathogen interactions. In this study, we used RNA sequencing to investigate host gene expression in asymptomatic avocado nursery trees infected with ASBVd. Transcriptome data showed that 631 genes were differentially expressed, 63 % of which were upregulated during infection. Plant defence responses, phytohormone networks, gene expression pathways, secondary metabolism, cellular transport as well as protein modification and degradation were all significantly affected by ASBVd infection. This work represents the first global gene expression study of ASBVd-infected avocado, and the transcriptional reprogramming observed during this asymptomatic infection improves our understanding of the molecular interactions underlying broader avsunviroid-host interactions.

Pest categorisation of the avocado sunblotch viroid

The EFSA Panel on Plant Health conducted a pest categorisation of the avocado sunblotch viroid (ASBVd) for the EU. The identity of ASBVd, a member of the genus Avsunviroid (family Avsunviroidae) is clearly defined and detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. ASBVd has been reported in Australia, Ghana, Guatemala, Israel, Mexico, Peru, South Africa, USA (California, Florida) and Venezuela. In the EU, it has been reported in Greece (Crete Island) and Spain. The pathogen could establish in the EU wherever avocado (Persea americana) is grown. The only known natural host of ASBVd is avocado to which it causes the severe 'avocado sunblotch' disease, characterised by white, yellow, red or necrotic depressed areas or scars on the fruit surface, bleached veins and petioles of the leaf, and rectangular cracking patterns in the bark of the old branches. Fruit yield and quality are severely diminished. ASBVd infects under experimental conditions a few more species in the family Lauraceae. The viroid is naturally transmitted at an extremely high rate by seeds (up to 100% in asymptomatically infected trees), but with a low efficiency by pollen (only to the produced seeds), and possibly through root grafts. Plants for planting, including seeds, and fresh avocado fruits were identified as the most relevant pathways for further entry of ASBVd into the EU. Avocado crops are cultivated in southern EU countries. Should the pest further enter and establish in the EU, impact on the production of avocado is expected. Phytosanitary measures are available to prevent entry and spread of the viroid in the EU. ASBVd fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods to Reveal Genetic Variability Within a Virus Species

The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (<500 bases in length) genomic regions of viral genomes. The different steps of SNaPshot and CE-SSCP setup procedures are presented using Potato virus Y (PVY, Potyvirus) and Plum pox virus (PPV, Potyvirus) RNA viruses as molecular targets, respectively.

Small RNA-mediated regulation of host-pathogen interactions

The rise in antimicrobial drug resistance, alongside the failure of conventional research to discover new antibiotics, will inevitably lead to a public health crisis that can drastically curtail our ability to combat infectious disease. Thus, there is a great global health need for development of antimicrobial countermeasures that target novel cell molecules or processes. RNA represents a largely unexploited category of potential targets for antimicrobial design. For decades, control of cellular behavior was thought to be the exclusive purview of protein-based regulators. The recent discovery of small RNAs (sRNAs) as a universal class of powerful RNA-based regulatory biomolecules has the potential to revolutionize our understanding of gene regulation in practically all biological functions. In general, sRNAs regulate gene expression by base-pairing with multiple downstream target mRNAs to prevent translation of mRNA into protein. In this review, we will discuss recent studies that document discovery of bacterial, viral, and human sRNAs and their molecular mechanisms in regulation of pathogen virulence and host immunity. Illuminating the functional roles of sRNAs in virulence and host immunity can provide the fundamental knowledge for development of next-generation antibiotics using sRNAs as novel targets.

Fluorescent-based techniques for viral detection, quantification, and characterization

Fluorescent-based technologies offer opportunities for developing new assays for detection, quantification, and characterization of viral isolates. According to the intrinsic characteristics of fluorescent-based tools (high specificity, sensitivity, and reliability), such type of molecular assays makes possible investigations on original studies such as evolutionary processes (including fitness measurement of isolates), quantitative epidemiology, or the analysis of synergism and antagonism between closely related isolates. The development of these tools is very simple and requires, in complement to basic molecular knowledge such as extraction, cloning, and (RT)-PCR procedures, only the identification of short specific sequence(s) in the targeted viral genome. The Single Nucleotide Polymorphism (SNP) and the 'real-time' RT-PCR assays are proposed as fluorescent-based tools for qualitative and quantitative viral detection, respectively. Moreover, the SNaPshot technology is described as method for isolate characterization.

Analysis of population structures of viral isolates using single-strand conformation polymorphism method

The analysis of viral populations requires the use of techniques that describe characteristics of individuals. The single-strand conformation polymorphism (SSCP) makes possible the identification of genetic differences between viral sequences and constitutes an alternative to the expensive and time-consuming cloning and sequencing strategies. Applied to small genomic regions (from 100 to 500 bases in length), SSCP patterns could describe, under appropriate experimental conditions, single nucleotide variations in the studied sequence. The different steps of a complete SSCP procedure, from sampling to pattern analysis (including nucleic acid extraction, RT-PCR amplification, double-stranded DNA quantification, polyacrylamide gel preparation, electrophoresis conditions, and staining procedures), are described using a region (500 bases) of the barley yellow dwarfvirus-PAV (BYDV-PAV, Luteovirus) genome as molecular target.

Viroid: a useful model for studying the basic principles of infection and RNA biology

Viroids are small, circular, noncoding RNAs that currently are known to infect only plants. They also are the smallest self-replicating genetic units known. Without encoding proteins and requirement for helper viruses, these small RNAs contain all the information necessary to mediate intracellular trafficking and localization, replication, systemic trafficking, and pathogenicity. All or most of these functions likely result from direct interactions between distinct viroid RNA structural motifs and their cognate cellular factors. In this review, we discuss current knowledge of these RNA motifs and cellular factors. An emerging theme is that the structural simplicity, functional versatility, and experimental tractability of viroid RNAs make viroid-host interactions an excellent model to investigate the basic principles of infection and further the general mechanisms of RNA-templated replication, intracellular and intercellular RNA trafficking, and RNA-based regulation of gene expression. We anticipate that significant advances in understanding viroid-host interactions will be achieved through multifaceted secondary and tertiary RNA structural analyses in conjunction with genetic, biochemical, cellular, and molecular tools to characterize the RNA motifs and cellular factors associated with the processes leading to systemic infection.

Single-strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis

We investigated the reliability of capillary array electrophoresis-single strand conformation polymorphism (CAE-SSCP) to determine if it can be used to identify novel alleles of candidate genes in a germplasm collection. Both strands of three different size fragments (160, 245 and 437 bp) that differed by one or more nucleotides in sequence were analyzed at four different temperatures (18 degrees C, 25 degrees C, 30 degrees C, and 35 degrees C). Mixtures of amplified fragments of either the intron interrupting the C-terminal WRKY domain of the Tc10 locus or the NBS domain of the TcRGH1 locus of Theobroma cacao were electroinjected into all 16 capillaries of an ABI 3100 Genetic Analyzer and analyzed three times at each temperature. Multiplexing of samples of different size range is possible, as intermediate and large fragments were analyzed simultaneously in these experiments. A statistical analysis of the means of the fragment mobilities demonstrated that single-stranded conformers of the fragments could be reliably identified by their mobility at all temperatures and size classes. The order of elution of fragments was not consistent over strands or temperatures for the intermediate and large fragments. If samples are only run once at a single temperature, small fragments could be identified from a single strand at a single temperature. A combination of data from both strands of a single run was needed to identify correctly all four of the intermediate fragments and no combination of data from strands or temperatures would allow the correct identification of two large fragments that differed by only a single single-nucleotide polymorphism (SNP) from a single run. Thus, to adequately assess alleles at a candidate gene locus using SSCP on a capillary array, fragments should be < or =250 bp, samples should be analyzed at two different temperatures between 18 degrees C and 30 degrees C to reduce the variability introduced by the capillaries, data should be combined from both strands and both temperatures, and undenatured double-stranded (ds)DNA molecular weight standards, such as ROX 2500, should be included as internal standards.