Next-Generation Sequencing and Genome Editing in Plant Virology

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.

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

“…To answer these questions we used a viral metagenomic approach using next generation sequencing (NGS) on symptomatic beans and cowpeas. NGS applications in plant virology began in 2009 (Blawid, Silva and Nagata, 2017) and have been increasingly applied in the de novo discovery of RNA and DNA viruses as well as viroids due to its rise as a rapid and relatively inexpensive mode of viral detection (Hadidi et al 2016; Blawid, Silva and Nagata, 2017). Previous reports of using NGS for novel viral discovery and subsequent evolutionary analysis are well-documented (Kehoe et al 2014; Alicai et al 2016; Ndunguru et al 2015; Wamonje et al 2017; Maina et al 2017; Kraberger et al 2017).…”

Diseases of Cashew Nut Plants (Anacardium Occidentale L.) in Burkina Faso

“…Unfortunately, cashew is threatened by many biotic and abiotic constraints resulting in significant yield losses. Among biotic constraints, diseases and pests are the most damaging and compromise the cashew nut yield in terms of quality and quantity [4][5][6][7][8][9][10][11][12][13][14][15]. Indeed, more than 12 diseases were reported to infect cashew tree worldwide.…”

Recent advances and prospects in Prunus virology

“…Hadidi et al . () showed the important role of NGS in the last 7 years regarding pathogen–virus interaction, describing how this technology could connect plant virology with genome editing, which could be really powerful together thanks to their synergy. Genome editing will certainly become a powerful tool in plant virology in the coming years thanks to the genome engineering method known as CRISPR‐Cas (clustered regularly interspaced short palindromic repeats and their associated Cas proteins).…”