Characterization of Spanish Olive Virome by High Throughput Sequencing Opens New Insights and Uncertainties

Abstract

The use of high throughput sequencing (HTS) for the analysis of Spanish olive trees showing leaf yellowing discoloration, defoliation, and/or decline has provided new insights into the olive viruses present in Spain and has opened discussions about the pros and cons of these technologies for diagnostic purposes. In this study, we report for the first time in Spanish orchards the presence of olive leaf yellowing-associated virus (OLYaV), for which the second full coding sequence has been determined. This virus has also been detected in a putative vector, the psyllid Euphyllura olivina. In addition, the presence in Spain of Olea europaea geminivirus (OEGV), recently reported in Italy, has been confirmed, and the full-length sequence of two isolates was obtained by HTS and Sanger sequencing. These results, as well as the detection of other viral sequences related to olive latent virus 3 (OLV-3) and olive viral satellite RNA, raises questions on the biological significance of the findings, about the requirement of standardization on the interpretation of HTS results, and the necessity of additional tests to confirm the relevance of the HTS detection of viral sequences.

Development of a Real-Time Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Olea Europaea Geminivirus

“…In particular, this method represents a potential tool for rapidly screening olive plant material useful for large surveys of the spread and pathogenicity of this virus, which to date remain uncertain. Interestingly, as recently reported by Ruiz-García and co-workers [ 18 ], the high level of sequence conservation encountered among all OEGV accession so far isolated requires a prompt investigation of the evolutionary and biological significance of this geminivirus in olive, opening new scenarios about its mechanisms of spread in the major olive-growing areas of the world.…”

“…The identification of this new virus was facilitated by HTS, a technique that allows for the discovery of new plant viruses, especially when symptoms are not evident, as is the case of OEGV. Besides Apulia, OEGV was recently reported in different areas where the olive cultivation is widespread [ 15 , 17 , 18 ].…”

“…In the last year, thanks also to the application of new technologies such as high-throughput sequencing (HTS), a new geminivirus called Olea europaea geminivirus (OEGV) has been identified in the olive tree [ 16 ], but its spread and pathogenicity remain puzzling. Since its first identification in Apulia [ 16 ] in the “Ogliarola” and “Leccino” cvs, OEGV was reported in California and Texas [ 17 ], Portugal [ 15 ], and Spain [ 18 ]. OEGV is classified as a putative member within the Geminiviridae family [ 16 ], currently including 14 genera [ 19 ] and few other still unassigned geminiviruses [ 20 ].…”

“…In a recent survey, Alabi and co-workers [ 17 ] detected OEGV-positive olive trees originating from different locations, advancing the concept of a possible worldwide spread of this virus, likely due to the inadvertent movement of germplasms from clonally propagated infected but asymptomatic olive trees. As a matter of fact, OEGV does not appear to be clearly associated to any symptom in olive; moreover, a high degree of sequence conservation has been identified [ 18 ].…”

Identification and complete genome sequencing of a divergent olive virus T isolate and an olive leaf yellowing-associated virus isolate naturally infecting olive trees in Greece

“…Over the last decade, the wide application of high-throughput sequencing (HTS) has allowed the rapid identification and characterization of several novel or new strains of known viruses in various plant species using different technologies [7][8][9][10]. Hence, in olive, new viral agents have also come up or divergent variants of known viral agents have been molecularly characterized with the application of HTS [5,6,11,12].…”