Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
Highlights
Fruit trees host a wide range of viral pathogens, mainly as a result of their vegetative mode of propagation and perennial nature [1]
Illumina offers nine different sequencers (Table 1) that can produce from 4 million to 20 billion short reads, from 50 to 300 nucleotides. It is the most used technology in fruit tree virus research, and couples sequencing-by-synthesis on a surface of a flow cell divided in lanes
High-Throughput Sequencing Methodology Applied to the Detection of Fruit Tree Viruses
Summary
Fruit trees host a wide range of viral pathogens, mainly as a result of their vegetative mode of propagation and perennial nature [1]. Similar situations occurred with well-known and widely spread viruses, such as Prune dwarf virus (PDV) [26] and Apple chlorotic leaf spot virus (ACLSV) [27], highlighting the need for continuous assessment of the viral molecular variability as a prerequisite to develop polyvalent and efficient detection tools. Such problems can be overcome by the use of modern generation sequencing (NGS) or high-throughput sequencing (HTS) technologies, which, theoretically, can produce sequence data of every putative viral agent present in a sample without the need of any former knowledge about their genome [28]. This fact, in addition to the relatively little time needed for the completion of a sequence run and the analysis of the resulting data, make HTS the undisputed leading technology in diagnostics, nowadays
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