Abstract
The early 1970s marked two breakthroughs in the field of biology: (i) The development of nucleotide sequencing technology; and, (ii) the discovery of the viroids. The first DNA sequences were obtained by two-dimensional chromatography which was later replaced by sequencing using electrophoresis technique. The subsequent development of fluorescence-based sequencing method which made DNA sequencing not only easier, but many orders of magnitude faster. The knowledge of DNA sequences has become an indispensable tool for both basic and applied research. It has shed light biology of viroids, the highly structured, circular, single-stranded non-coding RNA molecules that infect numerous economically important plants. Our understanding of viroid molecular biology and biochemistry has been intimately associated with the evolution of nucleic acid sequencing technologies. With the development of the next-generation sequence method, viroid research exponentially progressed, notably in the areas of the molecular mechanisms of viroids and viroid diseases, viroid pathogenesis, viroid quasi-species, viroid adaptability, and viroid–host interactions, to name a few examples. In this review, the progress in the understanding of viroid biology in conjunction with the improvements in nucleotide sequencing technology is summarized. The future of viroid research with respect to the use of third-generation sequencing technology is also briefly envisaged.
Highlights
Since the discovery of viroids 53 years ago [1], they have remained one of the most fascinating biological molecules as they are the smallest known infectious RNA molecules (246 to 434 nucleotides) and are capable of autonomous self-replication without coding for any peptides
Studies on viroids led to the discovery of some of the most interesting features in RNA biology, things such as the fact that non-translatable RNA can cause disease, that viroids are very small in size and possess a circular genome, and that they possess self-cleavage structures [4]
Research on viroids resulted in the development of several innovative methods such as nucleic acid purification and gel electrophoresis that became standard protocols that were subsequently used to confirm that prions are infectious proteins that are devoid of any nucleic acids [5]
Summary
Since the discovery of viroids 53 years ago [1], they have remained one of the most fascinating biological molecules as they are the smallest known infectious RNA molecules (246 to 434 nucleotides (nt)) and are capable of autonomous self-replication without coding for any peptides. The research findings of Theodor Diener and William Raymer showed that the causative agent was protein-free RNA molecule 50–80 times smaller than the smallest known viral genomes This agent, the first-ever reported “viroid” (term coined in the year 1971), was eventually named the potato spindle tuber viroid (PSTVd) [1,7]. The exponential evolution in genomics driven by the development of the polymerase chain reaction (PCR), high-quality enzymes and the development of fluorescent automated DNA sequencing technologies rapidly contributed to the understanding of viroid biology This led to the detection of several thousand viroid sequence variants that infect several plant species. The rapid evolution of biological tools, techniques and instruments has led to constant changes in sequencing technology, changes which are further helped by the ever-evolving analysis algorithms being developed All of this creates substantial challenges as well as discoveries in viroid research. - Effect of viroid infection host genome: Transcriptome analysis and degradation studies
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