Impact of Nucleic Acid Sequencing on Viroid Biology

• Published in: International journal of molecular sciences Vol. 21; no. 15; p. 5532
• Main Authors: Adkar-Purushothama, Charith Raj, Perreault, Jean-Pierre
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01-08-2020; MDPI
• Subjects: Adaptability; Analytical chemistry; Biology; Biomedical Research - methods; Biomedical Research - trends; Deoxyribonucleic acid; DNA; DNA sequencing; Electrophoresis; Evolution; Fluorescence; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - trends; Host-Pathogen Interactions; Models, Genetic; Molecular biology; Molecular modelling; Next-generation sequencing; Non-coding RNA; Nucleic Acids - analysis; Nucleic Acids - genetics; Nucleotide sequence; Nucleotides; Pathogenesis; Pathogens; Plant Diseases - virology; Plant Viruses - classification; Plant Viruses - genetics; Potatoes; Proteins; Researchers; Review; RNA, Viral - analysis; RNA, Viral - genetics; third generation sequencing; Transfer RNA; Viroids; Viroids - genetics; Virus Replication - genetics; North America; non-coding RNA; next-generation sequencing; third generation sequencing; viroids; DNA sequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms21155532

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.