Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21–24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
Highlights
The field of virology was born in the late 1890s when it was found that the tobacco mosaic disease is caused by a novel form of infectious agent named “ultravirus” and referred to as ‘contagium vivum fluidum’
For the last seven years, Next-generation sequencing (NGS) and bioinformatics have provided rapid and low cost DNA and/or RNA sequencing for plant viruses and viroids
Using NGS in a quarantine program, a novel virus in imported sugarcane was discovered that previously escaped detection by standard detection methods
Summary
The field of virology was born in the late 1890s when it was found that the tobacco mosaic disease is caused by a novel form of infectious agent named “ultravirus” and referred to as ‘contagium vivum fluidum’ (soluble living germ or contagious living fluid; Hadidi and Barba, 2012). Some viruses and viroids can be largely latent (symptomsless) in some of their infected hosts (Hadidi et al, 1998, 2003, 2011) These latent agents, may be pathogenic in other hosts and their infections may result in yield reduction and general weakness of plants (Hadidi et al, 1998, 2003, 2011; Hadidi and Barba, 2012; Barba et al, 2015). In this article we discuss the progress made in plant virology during the last 7 years by NGS and very recently by CRISPR-Cas systems
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