Next-Generation Sequencing and CRISPR-Cas Editing in Plant Virology

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Background

Advances in next-generation sequencing (NGS) capabilities and the discovery during the last few years that bacteria and archaea have heritable adaptive immunity mediated through Clustered Regularly Interspaced Short Palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably DNA and RNA sequencing, gene and genome editing as well as molecular diagnostics. NGS combined with informatics has been applied to plant viruses and viroids for a decade. NGS provides highly efficient, rapid, low cost high-throughput sequencing of virus and viroid genomes and of the 21-24 nucleotides pathogen-derived small RNAs generated during the infection process. These sRNAs, cover frequently the whole virus or viroid genome. NGS has been used in a number of virus and viroid studies including, but not limited to, discovery of novel viruses and viroids or their variants, detection and identification of known pathogens, extending the known virus or viroid host range, pathogen-host interactions, pathogen evolution and pathogenesis, mRNA targeting, symptom expression, and others. The CRISPR-Cas systems have been applied to plant viruses for four years. The application to the ssDNA geminiviruses has been shown to enhance resistance to tomato yellow leaf curl virus, bean yellow dwarf virus, beet severe curly top virus and wheat dwarf virus which belong to different genera. Moreover, CRISPR-Cas editing of the endogenous dsDNA banana streak virus (family, Caulimoviridae) in the B genome of Musa spp. has overcome a major challenge in banana breeding. In addition, CRISPR-Cas editing has been used successfully to target two sites of the plant elF4E gene function in cucumber to develop plants resistant to three ssRNA viruses, members of the family Potyviridae, namely cucumber vein yellowing virus, papaya ringspot virus-w and zucchini yellow mosaic virus. Complete resistance to turnip mosaic virus, a member of the same family, was obtained when the CRISPR-Cas system targeted the plant elf (iso) 4E gene. Direct targeting of ssRNA of cucumber mosaic virus, tobacco mosaic virus or turnip mosaic virus has been recently successful in producing virus-resistant plants.

This Research Topic welcomes high-quality manuscripts (research papers, review articles or others) focusing on, but not limited to:
-Utilization of next-generation sequencing in research and diagnosis of plant viruses, viroids, plant viral satellites, fungal viruses and green algae viruses.
-Direct targeting of specific nucleotide sites of plant ssDNA viruses and viroids by the latest state-of-the art CRISPR-based genome editing technologies to enable the fast introduction of efficient resistance against infection by these pathogens
-Targeting sites of specific plant genes such as elF4E gene or elf (iso) 4E gene by CRISPR-Cas editing to develop plants resistant to ssRNA viruses.
-Since the CRISPR-Cas systems have been utilized recently for detection of human DNA and ssRNA viruses in a single reaction by visual read out in less than 1.5 h, multitarget DNA or RNA tests by the CRISPR-Cas systems have a good potential for their application as rapid and accurate diagnostic assays for plant viruses and viroids which will revolutionize the identification and detection method of these pathogens.

Keywords: Next-generation sequencing, genome editing, CRISPR-Cas systems, plant viruses, viroids

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