Impact of Nucleic Acid Sequencing on Viroid Biology

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.

A Current Overview of Two Viroids Prevailing in Citrus Orchards: Citrus Exocortis Viroid and Hop Stunt Viroid

“…Next-generation sequencing (NGS) technologies are currently becoming routinely applied in different fields of virus and viroids studies. These advanced technologies have therefore contributed to a revolution in both the detection and discovery of plant viruses and viroids [78][79][80][81]. NGS has also provided an alternative method to identify viroids in the citrus cultivars.…”

An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids

“…The Coleviroid species are devoid of TCR and TCH [ 65 ]. Figure 1 exemplifies the various structures adopted by these viroids [ 66 ].…”

“… Structural differences among viroids. (Adapted from Adkar-Purushothama and Perreault, 2020 [ 66 ]). Primary and secondary structural characteristics considered for classification of viroids: ( A ) the PSTVd rod-like secondary structure comprising five functional domains is shown: the Terminal left (TL), Pathogenicity (P), Central (C), Variable (V) and Terminal right (TR) domains are separated by solid vertical lines.…”

sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling

“…Viroid researchers extensively use NGS to study host–viroid interactions, focusing on vd-sRNA production [ 20 ]. The profiling of vd-sRNAs on both the genomic and antigenomic strands of a viroid yields several types of information, including, but not limited to: (i) the proportions of vd-sRNAs produced from the genomic and the antigenomic strands of the viroid, respectively; (ii) the distribution of vd-sRNAs on both the genomic and the antigenomic strands; and, (iii) the regions of the viroid that are either susceptible to or resist the host’s RNA silencing machinery.…”