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Viruses 2018, 10(8), 436; https://doi.org/10.3390/v10080436

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

1
Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2
Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy
3
Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain
4
Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
*
Author to whom correspondence should be addressed.
Received: 23 July 2018 / Revised: 9 August 2018 / Accepted: 13 August 2018 / Published: 17 August 2018
(This article belongs to the Special Issue Fruit Tree Viruses and Viroids)
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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. View Full-Text
Keywords: high-throughput sequencing; fruit trees; new viruses; detection; variability; siRNAs; total RNA; dsRNA high-throughput sequencing; fruit trees; new viruses; detection; variability; siRNAs; total RNA; dsRNA
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Maliogka, V.I.; Minafra, A.; Saldarelli, P.; Ruiz-García, A.B.; Glasa, M.; Katis, N.; Olmos, A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018, 10, 436.

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